Tag Archives: hydrogen bond

Much of the chemistry you learned is wrong

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When you were in school, you probably learned that understanding chemistry involved understanding the bonds between atoms. That all the things of the world were made of molecules, and that these molecules were fixed proportion combinations of the chemical elements held together by one of the 2 or 3 types of electron-sharing bonds. You were taught that water was H2O, that table salt was NaCl, that glass was SIO2, and rust was Fe2O3, and perhaps that the bonds involved an electron transferring between an electron-giver: H, Na, Si, or Fe… to an electron receiver: O or Cl above.

Sorry to say, none of that is true. These are fictions perpetrated by well-meaning, and sometime ignorant teachers. All of the materials mentioned above are grand polymers. Any of them can have extra or fewer atoms of any species, and as a result the stoichiometry isn’t quite fixed. They are not molecules at all in the sense you knew them. Also, ionic bonds hardly exist. Not in any chemical you’re familiar with. There are no common electron compounds. The world works, almost entirely on covalent, shared bonds. If bonds were ionic you could separate most materials by direct electrolysis of the pure compound, but you can not. You can not, for example, make iron by electrolysis of rust, nor can you make silicon by electrolysis of pure SiO2, or titanium by electrolysis of pure TiO. If you could, you’d make a lot of money and titanium would be very cheap. On the other hand, the fact that stoichiometry is rarely fixed allows you to make many useful devices, e.g. solid oxide fuel cells — things that should not work based on the chemistry you were taught.

Iron -zinc forms compounds, but they don't have fixed stoichiometry. As an example the compound at 60 atom % Zn is, I guess Zn3Fe2, but the composition varies quite a bit from there.

Iron -zinc forms compounds, but they don’t have fixed stoichiometry. As an example the compound at 68-80 atom% Zn is, I guess Zn7Fe3 with many substituted atoms, especially at temperatures near 665°C.

Because most bonds are covalent many compounds form that you would not expect. Most metal pairs form compounds with unusual stoicheometric composition. Here, for example, is the phase diagram for zinc and Iron –the materials behind galvanized sheet metal: iron that does not rust readily. The delta phase has a composition between 85 and 92 atom% Zn (8 and 15 a% iron): Perhaps the main compound is Zn5Fe2, not the sort of compound you’d expect, and it has a very variable compositions.

You may now ask why your teachers didn’t tell you this sort of stuff, but instead told you a pack of lies and half-truths. In part it’s because we don’t quite understand this ourselves. We don’t like to admit that. And besides, the lies serve a useful purpose: it gives us something to test you on. That is, a way to tell if you are a good student. The good students are those who memorize well and spit our lies back without asking too many questions of the wrong sort. We give students who do this good grades. I’m going to guess you were a good student (congratulations, so was I). The dullards got confused by our explanations. They asked too many questions, and asked, “can you explain that again? Or why? We get mad at these dullards and give them low grades. Eventually, the dullards feel bad enough about themselves to allow themselves to be ruled by us. We graduates who are confident in our ignorance rule the world, but inventions come from the dullards who don’t feel bad about their ignorance. They survive despite our best efforts. A few more of these folks survive in the west, and especially in America, than survive elsewhere. If you’re one, be happy you live here. In most countries you’d be beheaded.

Back to chemistry. It’s very difficult to know where to start to un-teach someone. Lets start with EMF and ionic bonds. While it is generally easier to remove an electron from a free metal atom than from a free non-metal atom, e.g. from a sodium atom instead of oxygen, removing an electron is always energetically unfavored, for all atoms. Similarly, while oxygen takes an extra electron easier than iron would, adding an electron is energetically unfavored. The figure below shows the classic ion bond, left, and two electron sharing options (center right) One is a bonding option the other anti-bonding. Nature prefers this to electron sharing to ionic bonds, even with blatantly ionic elements like sodium and chlorine.

Bond options in NaCl. Note that covalent is the stronger bond option though it requires less ionization.

Bond options in NaCl. Note that covalent is the stronger bond option though it requires less ionization.

There is a very small degree of ionic bonding in NaCl (left picture), but in virtually every case, covalent bonds (center) are easier to form and stronger when formed. And then there is the key anti-bonding state (right picture). The anti bond is hardly ever mentioned in high school or college chemistry, but it is critical — it’s this bond that keeps all mater from shrinking into nothingness.

I’ve discussed hydrogen bonds before. I find them fascinating since they make water wet and make life possible. I’d mentioned that they are just like regular bonds except that the quantum hydrogen atom (proton) plays the role that the electron plays. I now have to add that this is not a transfer, but a covalent spot. The H atom (proton) divides up like the electron did in the NaCl above. Thus, two water molecules are attracted by having partial bits of a proton half-way between the two oxygen atoms. The proton does not stay put at the center, there, but bobs between them as a quantum cloud. I should also mention that the hydrogen bond has an anti-bond state just like the electron above. We were never “taught” the hydrogen bond in high school or college — fortunately — that’s how I came to understand them. My professors, at Princeton saw hydrogen atoms as solid. It was their ignorance that allowed me to discover new things and get a PhD. One must be thankful for the folly of others: without it, no talented person could succeed.

And now I get to really weird bonds: entropy bonds. Have you ever noticed that meat gets softer when its aged in the freezer? That’s because most of the chemicals of life are held together by a sort of anti-bond called entropy, or randomness. The molecules in meat are unstable energetically, but actually increase the entropy of the water around them by their formation. When you lower the temperature you case the inherent instability of the bonds to cause them to let go. Unfortunately, this happens only slowly at low temperatures so you’ve got to age meat to tenderize it.

A nice thing about the entropy bond is that it is not particularly specific. A consequence of this is that all protein bonds are more-or-less the same strength. This allows proteins to form in a wide variety of compositions, but also means that deuterium oxide (heavy water) is toxic — it has a different entropic profile than regular water.

Robert Buxbaum, March 19, 2015. Unlearning false facts one lie at a time.

yet another quantum joke

Why do you get more energy from a steak than from the same amount of hamburger?

 

Hamburger is steak in the ground state.

 

Is funny because….. it’s a pun on the word ground. Hamburger is ground-up meat, of course, but the reference to a ground state also relates to a basic discovery of quantum mechanics (QM): that all things exist in quantized energy states. The lowest of these is called the ground state, and you get less energy out of a process if you start with things at this ground state. Lasers, as an example, get their energy by electrons being made to drop to their ground state at the same time; you can’t get any energy from a laser if the electrons start in the ground state.

The total energy of a thing can be thought of as having a kinetic and a potential energy part. The potential energy is usually higher the more an item moves from its ideal (lowest potential point). The kinetic energies of though tends to get lower when more space is available because, from Heisenberg uncertainty, ∆l•∆v=h. That is, the more space there is, the less uncertainty of speed, and thus the less kinetic energy other things being equal. The ground energy state is the lowest sum of potential and kinetic energy, and thus all things occupy a cloud of some size, even at the ground state. Without this size, the world would cease to exist. Atoms would radiate energy, and shrink until they vanished.

In grad school, I got into understanding thermodynamics, transport phenomena, and quantum mechanics, particularly involving hydrogen. This lead to my hydrogen production and purification inventions, what my company sells.

Click here for a quantum cartoon on waves and particles, an old Heisenberg joke, or a joke about how many quantum mechanicians it takes to change a lightbulb.

R. E. Buxbaum, July 16, 2013. I once claimed that the unseen process that maintains existence could be called God; this did not go well with the religious.

 

Heisenberg joke and why water is wet

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I love hydrogen in large part because it is a quantum fluid. To explain what that means and how that leads to water being wet, let me begin with an old quantum physics joke.

Werner Heisenberg is speeding down a highway in his car when he’s stopped by a police officer. “Do you know how fast you were going?” asks the officer. “No idea” answers Heisenberg, “but I know exactly where I am.”

The joke relates to a phenomenon of quantum physics that states that the more precisely you can know the location of something, the less precisely you can infer the speed. Thus, the fact that Heisenberg knew precisely where he was implied that he could have no idea of the car’s speed. Of course, this uncertainty is mostly seen with small things like light and electrons –and a bit with hydrogen, but hardly at all with a car or with Dr. Heisenberg himself (and that’s why it’s funny).

This funky property is related to something you may have wondered about: why is water wet? That is, why does water cling to your hands or clothes while liquid teflon repels. Even further, you may have wondered why water is a liquid at normal conditions when H2S is a gas; H2S is a heavier analog, so if one of the two were a liquid, you’d think it was H2S.

Both phenomena are understood through hydrogen behaving as the quantum car above. Oxygen atoms are pretty small, and hydrogen atoms are light enough to start behaving in a quantum way. When a hydrogen atom attaches to an oxygen atom to form part of a water molecule, its location becomes fixed rather precisely. As a result, the hydrogen atom gains velocity (the hydrogen isn’t going anywhere with this velocity, and it’s sometimes called zero-point energy), but because of this velocity or energy, its bond to the oxygen becomes looser than it would be if you had heavier hydrogen. When the oxygen of another water molecule or of a cotton cellulose molecule comes close, the hydrogen starts to hop back and forth between the two oxygen atoms. This reduces the velocity of the hydrogen atom, and stabilizes the assemblage. There is now less kinetic energy (or zero-point energy) in the system, and this stability is seen as a bond that is caused not by electron sharing but by hydrogen sharing. We call the reasonably stable bond between molecules that share a hydrogen atom this way a “hydrogen bond.” (now you know).

The hydrogen bond is why water is a liquid and is the reason water is wet. The hydrogen atom jumping between water molecules stabilizes the liquid water more than it would stabilize liquid H2S. Since sulfur atoms are bigger than oxygen atoms, the advantage of hydrogen jumping is smaller. As a result, the heat of vaporization of water is higher than that of H2S, and water is a liquid at normal conditions while H2S is a gas.

Water sticks to cotton or your skin the same way, hydrogen atoms skip between the oxygen of water molecules and of these surfaces creating a bond. It is said to whet these surfaces, and the result is that water is found to be wet. Liquid teflon does not have hydrogen atoms that can jump so there is no band that could be made from that direction (there are some hydrogen atoms on the cotton that can jump to the teflon, but there is no advantage to bonding of this sort as there are only a few hydrogen atoms, and these already jump to other oxygens in the cotton. Thus, to jump to the teflon would mean breaking a bond with other oxygen atoms in the cotton — there would be no energy advantage. This then is just one of the reasons I love hydrogen: it’s a quantum-y material.