Ecce LUMO

Ecce Homo, Caravaggio (1605)

Behold the HOMO (Highest Occupied Molecular Orbital), seeking reception;
Behold the LUMO (Lowest Unoccupied Molecular Orbital), offering reception.

Chemical reactions are electronic transfers. I don't mean electronic transfers like PayPal is (although there are similarities between electricity and money). I mean electronic transfers like oxidations and reductions, substitutions, proton transfers--which all involve electron donors and acceptors.  I still think that BH₃NH₃ best illustrates how chemistry is like sex: link

Presumably, the chemistry of memory has some donor and acceptor aspect at the molecular level. Long term potentiation. Learning is also like transubstantiation--words becoming neuronal flesh and all that. But there is more to learning than replication.  As Plutarch noted, learning is less like bucket filling and more like igniting little fires; Jefferson echoed that same thought: knowledge is contagious.

Here are some mnemonics for today's lesson:

HOMO/LUMO
Donor/Acceptor
Base/Acid
nucleophile/electrophile
Plug/Socket
Hand/Glove
Foot/Shoe

You can guess the rest.

Bromine swings both ways when coupling with double bonds

Here's a little chemical example of my favorite dictum: polarization followed by attack, followed by depolarization.

In certain solvents, molecular bromine, Br₂, cracks apart into plus and minus ions: bromide and bromonium (note the cool use of the "ium" suffix for the positively charged ion):

Br—Br  —>  Br^-  +  Br⁺

Now Br₂ will add to ethylene to make ethylene dibromide, a useful pesticide, but the bromine and ethylene can't simply couple because it's forbidden. Instead, bromonium ion approaches ethylene, sucking at and polarizing her most available electrons (recall I deduced that ethylene was female here). Bromonium's negatively charged doppelgänger (umpolung!) then backside attacks the polarized ethylene, after which her electrons collapse into bromonium's clutches and the partners relax. Here's a visual:

Bondage Is A Two-Way Street

The simple "one-way" notion of chemical bonding described back here is part of the "lone pair theory" developed by G.N. Lewis and N.V. Sidgwick. According to that theory, a neutral molecule such as ammonia donates electrons from its lone pair to a metallic Lewis acid.  But things like ethylene, not having any lone pairs, confounded the theory, since they too formed neutral metal complexes very similar to ammonia-metal complexes.

In 1935, Linus Pauling introduced the novel concept of backbonding to explain the shorter than expected Ni-C bonds observed in the electron diffraction structure of Ni(CO)₄.  Like many concepts in chemistry, backbonding is better illustrated than described:

In this simplified scheme above, CO gives electronic juice to the metal's empty and receptive d-orbital (left-hand side). At the same time, the metal gives back electrons to the CO (right-hand side) using a different full d-orbital: the two sketches overlap. They are synergistic.

Sex, Blogs, and Videotapes

Most any lengthy composition has a sequence, including things as disparate as polymers, novels, films, or even a blog. All these different things are sequentially pieced together from smaller subunits. For polymers, the subunits are monomers, for novels they are alphabet characters, for films and videotapes, they are "frames," and for blogs, they are separate posts (which themselves comprise a smaller sequence of characters).

It might be fun to explore the mechanics of stringing together novels, films, and blogs, etc. For polymers, I already mentioned "step growth polymerization" back here, describing how Wallace Carothers mastered the art of making long-chain synthetic polymers like nylon and neoprene. One way for a non-chemist to visualize step-growth polymerization is to imagine a very large group of unattached people, each willing to reach out and join hands with another to begin forming a human chain. Imagine how this must work at the beginning of the process. All are separate. In a first step, two people get together, each joining just one hand to make a pair, but each leaving one hand free. Now that pair could get together with another like pair to make a chain of four, but it's unlikely to do so because in a sea of singletons it's far more likely that the first pair will just hook up with another single person to make a trio. Again, that's not a choice thing -- it's a statistical thing because the number of available singletons far exceeds the number of available pairs -- at first. Look at the chain growth profile labeled "step-growth" in this chart (the red curve): 

For step-growth polymerization, not until the very end of the coupling orgy do the relative amounts of already linked members far outnumber the available remaining singletons and the daisy-chaining really takes off because having consumed all the singletons, the short chains must join hands with the ends of other chains. In the graph, the step-growth mechanism is contrasted with the living chain growth mechanism (straight line) which grows steadily. An example of the living growth chain mechanism is the Zeigler-Natta mechanism mentioned back here. Comment threads on blogs are also like "living" polymers.

Taking a closer look at the handholding analogy, it's a sanitized whitewash of what's really going on. The monomers in nylon are really "gendered" i.e. there are two types of monomers being joined: there is a "male" monomer, 1,6-diaminohexane which looks like this:

and a female monomer, 1,6-dicarboxyhexane (also called adipic acid) which looks like this:

I've already called attention to the "male" nature of amines, and the "female" nature of acids here. If that analogy bothers you, think instead of plugs and sockets or hands and gloves.

Ethylene, Daughter of Ethyl

Factoid for the day:

In the mid-19th century, the suffix -ene (an Ancient Greek root added to the end of female names meaning "daughter of") was widely used to refer to a molecule or part thereof that contained one fewer hydrogen atoms than the molecule being modified. Thus, ethylene (C₂H₄) was the "daughter of ethyl" (C₂H₅). The name ethylene was used in this sense as early as 1852. Wiki link

I could blog all day about ethylene, but that factoid was something I didn't know until today. Ethyl has lots of sisters too like Propyl, Butyl (one of the But-sisters), and Pentyl, etc.

Ethylene is ready for her close-up now:

Hard And Soft Elements: Size Does Matter

Here's a great Periodic Table showing the relative sizes of common ions. Cations are shown in red, anions are in blue.

Click To Enlarge

Cool things to note:

• Ions in the same column get bigger as one moves down a column.
• Look how ginormous cesium (bottom left) and iodide (bottom right) are.
• Look how small some ions are (Be²⁺ in particular).
• Look how invisibly small the proton is because H⁺ has no electrons. Hydride, H^-, having two electrons, is comparatively huge. It's almost like the planets Mercury and Jupiter. I wrote about Dr. Proton and Mr. Hydride back here.

A chemist named Ralph Pearson invented the concept of Hard Soft Acid Base (HSAB) Theory in the 1960s.  According to Pearson, "hard" (small) acids like Li⁺, Be²⁺, etc., naturally prefer binding with "hard" (small) bases like [OH]^- and O^2-.  Likewise, "soft" (larger) acids like silver, Ag⁺ and mercury, Hg²⁺ (when they aren't found in their elemental state) will invariably be found with a "soft" base, i.e., sulfide, S^2-.

So it goes.

Funny story about Pearson.  I saw him speak once at a special symposium dedicated to Henry. Pearson caught everyone's attention when he showed up late in the middle of a talk, entering at the rear, striding to the front of the room escorted arm-in-arm by two beautiful 20-something women (they turned out to be his grand nieces or something but everybody else was thinking "hired").  The women were dressed for cocktails too, not for a roomful of chemistry geeks. Pearson made his entry, said his hellos, and announced that he was just testing his principle of maximum hardness.

Umpolung: The Strange Case of Dr. Proton and Mr. Hydride

Umpolung is a chemistry term meaning "reversal of polarity." This is a useful trick, to change something from having a plus charge to having a minus charge. Hydrogen is the simplest example and shows how the same element behaves differently depending on whether it is cloaked in electrons or not.

The promiscuous proton, H⁺, flits from base to base in water. But hydride (written as H^-), laden with two electrons, usually seeks an electrophile with which to couple irreversibly. If proton and hydride get together, they make little H₂'s.

Hydrogen usually appears on the upper far left side of the Periodic Table sitting above Li, Na, K,.., emphasizing its usual cationic (H⁺) character.  But umpolung explains why it's sometimes useful to think of hydrogen as belonging on the upper right side (next to He), sitting above the halogens, F, Cl, Br,.., emphasizing its anionic H^- = hydride ~ halide character.

Chemistry Is Like Sex: Coupling Illustrated

G.N. Lewis (I wrote about him back here) was from Berkeley and thus a bit more liberal when defining acids and bases: He gave more general definitions of them than Brønsted and Lowry did. And while more open-minded, Lewis was a bit of a chauvinist when he argued that a base's precious electrons helped "complete the octet" of an acid when they coupled.

Consider the coupling of a simple base, ammonia, with a simple Lewis acid, borane. If you're a jaded chemist who has "seen it all" you might consider just skipping to this link dealing with borane and ammonia making borazane as a hydrogen fuel energy source.

We already "know" what ammonia looks like here--but what about borane?  I wrote a bit about boron the element back here.  Turns out that the word "boron" is etymologically linked to the Arabic tongue as well, via the word borax.

Borane, BH₃, is a natural fit for ammonia's lone pair.  Consider its structure:

BH₃ looks a bit like NH₃ but completely lacks a lone pair.  BH₃ has only six surrounding electrons instead of eight and so is electronically unfulfilled. In a sense, it has a big hole in its middle. In the absence of an available lone pair, BH₃ readily dimerizes in a head-to-tail fashion with another sister BH₃ molecule to form B₂H₆. Here's an illustration of two BH₃'s getting it on together:

When NH₃ and BH₃ prepare to bond, a natural question is where should NH₃ put its lone pair?  BH₃ has what's called a "virtual orbital" (there's nothing virtuous about it).  A virtual orbital is just an empty electron orbital. Another name is a LUMO. Empty orbitals have metes and bounds, despite there being nothing there there. Here's a lurid depiction of borane's virtual orbital:

It's a bit hard to see in the depiction above but all three of borane's tripodal hydrogen limbs are squished flat into a planar configuration between the two swollen globes. The red and blue empty lobes are equivalent in the eyes of ammonia's incoming lone pair: Borane's empty orbital can be approached from above or below.  As the ammonia approaches one side of borane, one empty lobe enlarges to accept the lone pair while the other shrinks. Also, borane's little hydrogen limbs fold back away from the incoming lone pair to accommodate the fit.  The final coupling product looks like this:

BH₃, with the help of ammonia's lone pair, now has an octet of electrons. 

The Basics Of How Chemistry Is Like Sex

Anyone who has cleaned with Windex has whiffed ammonia, a substance with a rich and interesting history that includes its very name: link.  Note that ammonia was once called animal alkali. Muslims-in-science scholars should take note of the origin of the word alkali, but should take care not to get the concept of alkaline bases etymologically confused with that other Arabic word meaning base.

Ammonia gas easily condenses into a liquid when compressed (Albert Einstein and his erstwhile student Leó Szilárd once patented a refrigerator with no moving parts that used ammonia instead of freon). If Szilárd's idea had gone anywhere, he may not have bothered to have conceived the atomic bomb.

Ammonia has been variously depicted as NH₃ or better as :NH₃ or better still with its electron "lone pair" on full display, as:

The lobe-like appendage sticking up is called a "lone pair" because there are two electrons in the orbital and because they're not associated with any atom except nitrogen.  Some depictions of ammonia omit the lone pair but here I prefer the "fig leaf is off" depiction.

Ammonia is perpetually in search of an acid to quench its baser instincts. Given a proton like H⁺, ammonia and the proton instantly couple to make ammonium NH₄⁺ in which all four H's become equivalent. In a real sense, the incoming acid polarizes the other three H's, sucking electrons away from them, making them all more acidic.

Acerbic Wet

The Danes and the Brits pioneered graphic depictions of simple chemical reactivity. Brønsted and Lowry independently shocked early 20th century chemists with their notions of spontaneous self-ionization of water:

Brønsted-Lowry theory explains how even the purest distilled water conducts electricity (which requires something charged). In their scheme, one water acts like a base by accepting a proton, while the other one acts like an acid, donating a proton. The slight but measurable extent of such H-swapping is real enough--a normal glass of water has a measurable concentration of H₃O⁺ of about 10^-7 units or a pH of 7 (pH is like a Richter scale). An equal & countervailing amount of hydroxide, OH^- neutralizes the acid.

Now consider adding anything to that glass of water which increases the amount of H₃O⁺ (but not OH^-).  Such a thing which donates an H⁺ to a neutral water molecule is called an acid in English.  The Germans call them Säure, which is related to our word sour. Svante Arrhenius (the august savant who also thought up AGW), came up with the idea first.

Everything You Always Wanted to Know About Chemistry But Were Afraid To Ask

Chemistry is all about electrons. Electrons used to go by old-fashioned names like corpuscles and were once even thought to move like fluids in an ether. So chemistry is really all about atoms and molecular bodies exchanging precious electrons.

Most garden variety chemistry is unimolecular or bimolecular. Unimolecular chemistry is dissociative, which on the one hand sounds asocial but on the other hand really just means to come undone. Bimolecular chemistry is more about two things coming together. Molecular threesomes do occur but they are rare (as one can imagine) and are technically called termolecular reactions. Concerted orgies of four or more molecular bodies are mostly just pure fantasy, unless there is some sort of prior bondage involved as sometimes occurs amongst biomolecules.  We'll save that for another day and focus on just the basics.

When two atoms or molecular bodies get together to react, there's always a donor and an acceptor (of the precious electrons).  Now besides the obvious connotations of donor and acceptor, it also turns out that the electron donor and acceptor parts of molecules have certain shapes. You may have also heard tell about HOMO's and LUMO's but that's getting a bit too technical.  We'll save that for elective or advanced classes. Suffice to say that some molecules can be both donors and acceptors depending on the shapes and energy levels of the coupling partner(s).

Many of the concepts I've just introduced can be illustrated graphically. One of my personal favorites is the simple coupling of H₂ with O₂ to make water (or steam).  But it turns out that this simple reaction is "forbidden" and so unfit for the present discussion.  Meanwhile, here's a different diagram to wet your appetites: