Category Archives: Chemistry

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.

Change your underwear; of mites and men

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The underware bomber mites make it right.

Umar, the underwear bomber.

For those who don’t know it, the underwear bomber, Umar Farook Abdulmutallab, wore his pair of explosive underwear for 3 weeks straight before trying to detonate them while flying over Detroit in 2009. They didn’t go off, leaving him scarred for life. It’s quite possible that the nasty little mites that live in underwear stopped the underwear bomber. They are a main source of US allergens too.

Dust mite, skin, and pollen seen with a light microscope. Gimmie some skin.

Dust mite, skin, and pollen seen with a light microscope. Gimmie some skin.

If you’ve ever used an electron microscope to look at household objects, you’ll find them covered with brick-like flakes of dried out skin-cells: yours and your friends’. Each person sheds his or her skin every month, on average. The outer layer dries out and flakes off as new skin grows in behind it. Skin flakes are the single largest source of household dust, and if not for the fact that these flakes are the main food for mites, your house would be chock full of your left over skin. When sunlight shines in your window, you see the shimmer of skin-flakes hanging in the air. Under the electron microscope, the fresh skin flakes look like bricks, but mite-eaten skin flakes look irregular. Less common, but more busy are the mites.

The facial mite movie. They live on in us, about 1 per hair follicle, particularly favoring eyelashes. Whenever you shower, your shower with a friend.

The facial mite movie. They live on in us, about 1 per hair follicle, particularly favoring eyelashes. Whenever you shower, you shower with a friend.

Dry skin is mostly protein (keratin), plus cholesterol and squalene. This provides great nutrition for dust mites and their associated bacteria. In warm, damp environments, as in your underwear or mattress, these beasties multiply and eat the old skin. The average density of dust mites on a mattress is greater than 2500/gram of dust.[1]  The mites leave behind excrement and broken off mite-limbs: nasty bits that are the most common allergens in the US today.

An allergy to dust shows up as sneezing, coughing, clogged lungs, and eczema. The most effective cure is a high level of in-home hygiene; mites don’t like soap or dry air. You’ve go to mop and vacuum regularly. Clean and change your clothing, particularly your undergarments; rotate your mattresses, and shake the dust out of your bedding. Vacuuming is less-effective as a significant fraction of the nasties go through the filter and get spread around by the vacuum blower.

As it turns out, dust mites and their bacteria eat more than skin. They also eat dried body fluids, poop residue, and the particular explosive used by Umar Farook, pentaerythritol tetra nitrate, PETN (humans can eat and metabolize this stuff too — it’s an angina treatment). The mites turn PETN into less-explosive versions, plus more mites.

Mighty mites as seen with electron microscopy. They eat more than skin.

Mighty mites as seen with electron microscopy. They eat more than skin.

There are many varieties of mite living on and among us. Belly button mites, for example, and face mites as shown above (click on the image to see it move). On average, people have one facial mite per hair follicle. It’s also possible that the bomber was stopped by poor quality control engineering and not mites at all. Religion tends to be at odds with a science like quality control, and followers tend to put their faith in miracles.

Chigger turning on a dime

Chigger turning on a dime

larger than the dust mite is the chigger, shown at left. Chiggers leave visible bites, particularly along the underwear waste-band. There are larger-yet critters in the family: lice, bed bugs, crabs. Bathing regularly, and cleaning your stuff will rid yourself of all these beasties, at least temporarily. Keeping your hair short and your windows open helps too. Mites multiply in humid, warm environments. Opening the windows dries and cools the air, and blows out mite-bits that could cause wheezing. Benjamin Franklin and took air-baths too: walking around naked with the windows open, even in winter. It helped that he lived on the second floor. Other ways to minimize mite growth include sunlight, DOT (a modern version of DDT), and eucalyptus oil. At the very minimum, change your underwear regularly. It goes a long way to reduce dust embarrassing moments at the jihadist convention.

Dr. Robert E. Buxbaum, Sept 21, 2014. Not all science or life is this weird and wonderful, but a lot is, and I prefer to write about the weird and wonderful bits. See e.g. the hazards of health food, the value of sunshine, or the cancer hazard of living near a river. Or the grammar of pirates.

New mixed drink, the R°

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Earlier this week, R__ turned 21, the drinking age in most of the USA. As a gift to her, I thought I might invent a new mixed drink that would suit her taste, and make her birthday more special. My requirements: that it should be kosher, that it’s made with widely available ingredients; that it should be relatively sophisticated, that it should be lower in alcohol (a fatherly concern), and that it should taste good to her and the general public.

The R___: gin tonic and grenadine

The R°: gin, tonic , ice, and grenadine

What I came up with, is something I call,The R°. It’s a modification of one of the great drinks of the western world, the gin and tonic. My modification is to use less gin, and to use grenadine instead of the traditional squeeze of lime. As she gets older, she may want to increase the gin content. The recipe: put 2/3 shot gin in a 10 oz straight-sided glass. Fill the glass 2/3 full of ice, near-fill with tonic water, and add a dash of grenadine, 1/4 shot or so (I used Rose’s). Stir slightly so the pink color stays mostly on the bottom. The result is slightly sweeter than the traditional gin and tonic, kosher in almost all places (you’ve got to check, but generally true), fairly sophisticated, good-tasting, and a reminder of Israel, a country where pomegranates grow all over. If you order one at a place with black lights and doesn’t stir much,you’ll discover that the tonic water glows electric-blue.

The verdict: R__ liked it. My hope is that you will enjoy it too. As a literary note, grenade is French for pomegranate; hand grenades got their name because of the shape. This drink is also suitable for talk like a pirate day (September 19).

Sept 14, 2014. My only previous gastronomic post was a recipe to make great lemonade. For a song by my daughter, go here, or here. For a joke about a neutron walking into a bar, go here.

Toxic electrochemistry and biology at home

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A few weeks back, I decided to do something about the low quality of experiments in modern chemistry and science sets; I posted to this blog some interesting science experiments, and some more-interesting experiments that could be done at home using the toxic (poisonous dangerous) chemicals available under the sink or on the hardware store. Here are some more. As previously, the chemicals are toxic and dangerous but available. As previously, these experiments should be done only with parental (adult) supervision. Some of these next experiments involve some math, as key aspect of science; others involve some new equipment as well as the stuff you used previously. To do them all, you will want a stop watch, a volt-amp meter, and a small transformer, available at RadioShack; you’ll also want some test tubes or similar, clear cigar tubes, wire and baking soda; for the coating experiment you’ll want copper drain clear, or copper containing fertilizer and some washers available at the hardware store; for metal casting experiment you’ll need a tin can, pliers, a gas stove and some pennies, plus a mold, some sand, good shoes, and a floor cover; and for the biology experiment you will need several 9 V batteries, and you will have to get a frog and kill it. You can skip any of these experiments, if you like and do the others. If you have not done the previous experiments, look them over or do them now.

1) The first experiments aim to add some numerical observations to our previous studies of electrolysis. Here is where you will see why we think that molecules like water are made of fixed compositions of atoms. Lets redo the water electrolysis experiment now with an Ammeter in line between the battery and one of the electrodes. With the ammeter connected, put both electrodes deep into a solution of water with a little lye, and then (while watching the ammeter) lift one electrode half out, place it back, and lift the other. You will find, I think, that one of the other electrode is the limiting electrode, and that the amperage goes to 1/2 its previous value when this electrode is half lifted. Lifting the other electrode changes neither the amperage or the amount of bubbles, but lifting this limiting electrode changes both the amount of bubbles and the amperage. If you watch closely, though, you’ll see it changes the amount of bubbles at both electrodes in proportion, and that the amount of bubbles is in promotion to the amperage. If you collect the two gasses simultaneously, you’ll see that the volume of gas collected is always in a ratio of 2 to 1. For other electrolysis (H2 and Cl2) it will be 1 to1; it’s always a ratio of small numbers. See diagram below on how to make and collect oxygen and hydrogen simultaneously by electrolyzing water with lye or baking soda as electrolyte. With lye or baking soda, you’ll find that there is always twice as much hydrogen produced as oxygen — exactly.

You can also do electrolysis with table salt or muriatic acid as an electrolyte, but for this you’ll need carbon or platinum electrodes. If you do it right, you’ll get hydrogen and chlorine, a green gas that smells bad. If you don’t do this right, using a wire instead of a carbon or platinum electrode, you’ll still get hydrogen, but no chlorine. Instead of chlorine, you’ll corrode the wire on that end, making e.g. copper chloride. With a carbon electrode and any chloride compound as the electrolyte, you’ll produce chlorine; without a chloride electrolyte, you will not produce chlorine at any voltage, or with any electrode. And if you make chlorine and check the volumes, you’ll find you always make one volume of chlorine for every volume of hydrogen. We imagine from this that the compounds are made of fixed atoms that transfer electrons in fixed whole numbers per molecule. You always make two volumes of hydrogen for every volume of oxygen because (we think) making oxygen requires twice as many electrons as making hydrogen.

At home electrolysis experiment

At home electrolysis experiment

We get the same volume of chlorine as hydrogen because making chlorine and hydrogen requires the same amount of electrons to be transferred. These are the sort of experiments that caused people to believe in atoms and molecules as the fundamental unchanging components of matter. Different solutes, voltages, and electrodes will affect how fast you make hydrogen and oxygen, as will the amount of dissolved solute, but the gas produced are always the same, and the ratio of volumes is always proportional to the amperage in a fixed ratio of small whole numbers.

As always, don’t let significant quantities of use hydrogen and oxygen or pure hydrogen and chlorine mix in a closed space. Hydrogen and oxygen is quite explosive brown’s gas; hydrogen and chlorine are reactive as well. When working with chlorine it is best to work outside or near an open window: chlorine is a poison gas.

You may also want to try this with non-electrolytes, pure water or water with sugar or alcohol dissolved. You will find there is hardly any amperage or gas with these, but the small amount of gas produced will retain the same ratio. For college level folks, here is some physics/math relating to the minimum voltage and relating to the quantities you should expect at any amperage.

2) Now let’s try electro-plating metals. Using the right solutes, metals can be made to coat your electrodes the same way that bubbles of gas coated your electrodes in the experiments above. The key is to find the right chemical, and as a start let me suggest the copper sulphate sold in hardware stores to stop root growth. As an alternative copper sulphate is often sold as part of a fertilizer solution like “Miracle grow.” Look for copper on the label, or for a blue color fertilizer. Make a solution of copper using enough copper so that the solution is recognizably green, Use two steel washers as electrodes (that is connect the wires from your battery to the washers) and put them in the solution. You will find that one side turns red, as it is coated with copper. Depending on what else your copper solution contained, bubbles may appear at the other washer, or the other washer will corrode. 

You are now ready to take this to a higher level — silver coating. take a piece of silver plated material that you want to coat, and clean it nicely with soap and water. Connect it to the electrode where you previously coated copper. Now clean out the solution carefully. Buy some silver nitrate from a drug store, and dissolve a few grams (1/8 tsp for a start) in pure water; place the silverware and the same electrodes as before, connected to the battery. For a nicer coat use a 1 1/2 volt lantern battery; the 6 V battery will work too, but the silver won’t look as nice. With silver nitrate, you’ll notice that one electrode produces gas (oxygen) and the other turns silvery. Now disconnect the silvery electrode. You can use this method to silver coat a ring, fork, or cup — anything you want to have silver coated. This process is called electroplating. As with hydrogen production, there is a proportional relationship between the time, the amperage and the amount of metal you deposit — until all the silver nitrate in solution is used up.

As a yet-more complex version, you can also electroplate without using a battery. This was my Simple electroplating (presented previously). Consider this only after you understand most everything else I’ve done. When I saw this the first time in high school I was confused.

3) Casting metal objects using melted pennies, heat from a gas stove, and sand or plaster as a cast. This is pretty easy, but sort of dangerous — you need parents help, if only as a watcher. This is a version of an experiment I did as a kid.  I did metal casting using lead that some plumbers had left over. I melted it in a tin can on our gas stove and cast “quarters” in a plaster mold. Plumbers no longer use lead, but modern pennies are mostly zinc, and will melt about as well as my lead did. They are also much safer.

As a preparation for this experiment, get a bucket full of sand. This is where you’ll put your metal when you’re done. Now get some pennies (1970 or later), a pair of pliers, and an empty clean tin can, and a gas stove. If you like you can make a plaster mold of some small object: a ring, a 50 piece — anything you might want to cast from your pennies. With parents’ help, light your gas stove, put 5-8 pennies in the empty tin can, and hold the can over the lit gas burner using your pliers. Turn the gas to high. In a few minutes the bottom of the can will burn and become red-hot. About this point, the pennies will soften and melt into a silvery puddle. By tilting the can, you can stir the metal around (don’t get it on you!). When it looks completely melted you can pour the molten pennies into your sand bucket (carefully), or over your plaster mold (carefully). If you use a mold, you’ll get a zinc copy of whatever your mold was: jewelry, coins, etc. If you work at it, you’ll learn to make fancier and fancier casts. Adult help is welcome to avoid accidents. Once the metal solidifies, you can help cool it faster by dripping water on it from a faucet. Don’t touch it while it’s hot!

A plaster mold can be made by putting a 50¢ piece at the bottom of a paper cup, pouring plaster over the coin, and waiting for it to dry. Tear off the cup, turn the plaster over and pull out the coin; you’ve got a one-sided mold, good enough to make a one-sided coin. If you enjoy this, you can learn more about casting on Wikipedia; it’s an endeavor that only costs 4 or 5 cents per try. As a safety note: wear solid leather shoes and cover the floor near the stove with a board. If you drop the metal on the floor you’ll have a permanent burn mark on the floor and your mother will not be happy. If you drop hot metal on your you’ll have a permanent injury, and you won’t be happy. Older pennies are made of copper and will not melt. Here’s a video of someone pouring a lot of metal into an ant-hill (kills lots of ants, makes a mold of the hill).

It's often helpful to ask yourself, "what would Dr. Frankenstein do?"

It’s nice to have assistants, friends and adult help in the laboratory when you do science. Even without the castle, it’s what Dr. Frankenstein did.

4) Bringing a dead frog back to life (sort of). Make a high voltage battery of 45 to 90 V battery by attaching 5-10, 9V batteries in a daisy chain they will snap together. If you touch both exposed contacts you’ll give yourself a wicked shock. If you touch the electrodes to a newly killed frog, the frog legs will kick. This is sort of groovy. It was the inspiration for Dr. Frankenstein (at right), who then decides he could bring a person back from the dead with “more power.” Frankenstein’s monster is brought back to life this way, but ends up killing the good doctor. Shocks are sometimes helpful reanimating people stricken by heat attacks, and many buildings have shockers for this purpose. But don’t try to bring back the long-dead. By all accounts, the results are less-than pleasing. Try dissecting the rest of the frog and guess what each part is (a world book encyclopedia helps). As I recall, the heart keeps going for a while after it’s out of the frog — spooky.

5) Another version of this shocker is made with a small transformer (1″ square, say, radioshack) and a small battery (1.5-6V). Don’t use the 90V battery, you’ll kill someone. As a first version of this shocker, strip 1″ of  insulation off of the ends of some wire 12″ long say, and attach one end to two paired wires of the transformer (there will usually be a diagram in the box). If the transformer already has some wires coming out, all you have to do is strip more insulation off the ends so 1″ is un-inuslated. Take two paired ends in your hand, holding onto the uninsulated part and touch both to the battery for a second or two. Then disconnect them while holding the bare wires; you’ll get a shock. As a nastier version, get a friend to hope the opposite pair of wires on the uninsulated parts, while you hold the insulated parts of your two. Touch your two to the battery and disconnect while holding the insulation, you will see a nice spark, and your friend will get a nice shock. Play with it; different arrangements give more sparks or bigger shocks. Another thing you can do: put your experiment near a radio or TV. The transformer sparks will interfere with most nearby electronics; you can really mess up a computer this way, so keep it far from your computer. This is how wireless radio worked long ago, and how modern warfare will probably go. The atom bomb was detonated with a spark like this.

If you want to do more advanced science, it’s a good idea to learn math. This is important for statistics, for engineering, for quantum mechanics, and can even help for music. Get a few good high school or college books and read them cover to cover. An approach to science is to try to make something cool, that sort-of works, and then try to improve it. You then decide what a better version would work like,  modify your original semi-randomly and see if you’re going in the right direction. Don’t redesign with only one approach –it may not work. Read whatever you can, but don’t believe all you read. Often books are misleading, or wrong, and blogs are worse (I ought to know). When you find mistakes, note them in the margin, and try to explain them. You may find you were right, or that the book was right, but it’s a learning experience. If you like you can write the author and inform him/her of the errors. I find mailed letters are more respectful than e-mails — it shows you put in more effort.

Robert Buxbaum, February 20, 2014. Here’s the difference between metals and non-metals, and a periodic table cup that I made, and sell. And here’s a difference between science and religion – reproducibility.

Nerves are tensegrity structures and grow when pulled

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No one quite knows how nerve cells learn stuff. It is incorrectly thought that you can not get new nerves in the brain, nor that you can get brain cells to grow out further, but people have made new nerve cells, and when I was a professor at Michigan State, a Physiology colleague and I got brain and sensory nerves to grow out axons by pulling on them without the use of drugs.

I had just moved to Michigan State as a fresh PhD (Princeton) as an assistant professor of chemical engineering. Steve Heidemann was a few years ahead of me, a Physiology professor PhD from Princeton. We were both new Yorkers. He had been studying nerve structure, and wondered about how the growth cone makes nerves grow out axons (the axon is the long, stringy part of the nerve). A thought was that nerves were structured as Snelson-Fuller tensegrity structures, but it was not obvious how that would relate to growth or anything else. A Snelson-Fuller structure is shown below the structure stands erect not by compression, as in a pyramid or igloo, but rather because tension in the wires helps lift the metal pipes, and puts them in compression. The nerve cell, shown further below is similar with actin-protein as the outer, tensed skin, and a microtubule-protein core as the compress pipes. 

A Snelson-Fuller tensegrity sculpture in the graduate college courtyard at Princeton, where Steve and I got our PhDs

A Snelson-Fuller tensegrity sculpture in the graduate college courtyard at Princeton, an inspiration for our work.

Biothermodynamics was pretty basic 30 years ago (It still is today), and it was incorrectly thought that objects were more stable when put in compression. It didn’t take too much thermodynamics on my part to show otherwise, and so I started a part-time career in cell physiology. Consider first how mechanical force should affect the Gibbs free energy, G, of assembled microtubules. For any process at constant temperature and pressure, ∆G = work. If force is applied we expect some elastic work will be put into the assembled Mts in an amount  ∫f dz, where f is the force at every compression, and ∫dz is the integral of the distance traveled. Assuming a small force, or a constant spring, f = kz with k as the spring constant. Integrating the above, ∆G = ∫kz dz = kz2; ∆G is always positive whether z is positive or negative, that is the microtubule is most stable with no force, and is made less stable by any force, tension or compression. 

A cell showing what appears to be tensegrity. The microtubules in green surrounded by actin in red. If the actin is under tension the microtubules are in compression. From here.

A cell showing what appears to be tensegrity. The microtubules (green) surrounded by actin (red). In nerves Heidemann and I showed actin is in tension the microtubules in compression.

Assuming that microtubules in the nerve- axon are generally in compression as in the Snelson-Fuller structure, then pulling on the axon could potentially reduce the compression. Normally, this is done by a growth cone, we posited, but we could also do it by pulling. In either case, a decrease in the compression of the assembled microtubules should favor microtubule assembly.

To calculate the rates, I used absolute rate theory, something I’d learned from Dr. Mortimer Kostin, a most-excellent thermodynamics professor. I assumed that the free energy of the monomer was unaffected by force, and that the microtubules were in pseudo- equilibrium with the monomer. Growth rates were predicted to be proportional to the decrease in G, and the prediction matched experimental data. 

Our few efforts to cure nerve disease by pulling did not produce immediate results; it turns out to by hard to pull on nerves in the body. Still, we gained some publicity, and a variety of people seem to have found scientific and/or philosophical inspiration in this sort of tensegrity model for nerve growth. I particularly like this review article by Don Ingber in Scientific American. A little more out there is this view of consciousness life and the fate of the universe (where I got the cell picture). In general, tensegrity structures are more tough and flexible than normal construction. A tensegrity structure will bend easily, but rarely break. It seems likely that your body is held together this way, and because of this you can carry heavy things, and still move with flexibility. It also seems likely that bones are structured this way; as with nerves; they are reasonably flexible, and can be made to grow by pulling.

Now that I think about it, we should have done more theoretical or experimental work in this direction. I imagine that  pulling on the nerve also affects the stability of the actin network by affecting the chain configuration entropy. This might slow actin assembly, or perhaps not. It might have been worthwhile to look at new ways to pull, or at bone growth. In our in-vivo work we used an external magnetic field to pull. We might have looked at NASA funding too, since it’s been observed that astronauts grow in outer space by a solid inch or two, and their bodies deteriorate. Presumably, the lack of gravity causes the calcite in the bones to grow, making a person less of a tensegrity structure. The muscle must grow too, just to keep up, but I don’t have a theory for muscle.

Robert Buxbaum, February 2, 2014. Vaguely related to this, I’ve written about architecture, art, and mechanical design.

Toxic chemistry you can do at home

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I got my start on science working with a 7 chemical, chemistry set that my sister got me when I was 7 years old (thanks Beverly). The chemicals would never be sold by a US company today — too much liability. What if your child poisons himself/herself or someone else, or is allergic, or someone chokes on the caps (anything the size of a nut has to be labeled as a hazard). Many of the experiments were called magic, and they were, in the sense that, if you did them 200 years earlier, you’d be burnt as a witch. There were dramatic color changes (phenolphthalein plus base, Prussian Blue) a time-delay experiment involving cobalt, and even an experiment that (as I recall) burst into fire on its own (glycerine plus granulated potassium permanganate).

Better evil through science. If you get good at this, the military may have use of your services.

“Better the evil you know.” If you get good at this, the military may have use of your services. Yes, the American military does science.

Science kits nowadays don’t do anything magically cool like that, and they don’t really teach chemistry, either, I think. Doing magical things requires chemicals that are reasonably reactive, and that means corrosive and/or toxic. Current kits use only food products like corn-starch or baking soda, and the best you can do with these is to make goo and/ or bubbles. No one would be burnt at the stake for this, even 300 years ago. I suppose one could design a program that used these materials to teach something about flow, or nucleation, but that would require math, and the kit producers fear that any math will turn off kids and stop their parents from spending money. There is also the issue of motivation. Much of historical chemistry was driven by greed and war; these are issues that still motivate kids, but that modern set-makers would like to ignore. Instead, current kits are supposed to be exciting in a cooperative way (whatever that means), because the kit-maker says so. They are not. I went through every experiment in my first kit in the first day, and got things right within the first week — showing off to whoever would watch. Modern kits don’t motivate this sort of use; I doubt most get half-used in a lifetime.

There are some foreign-made chemistry sets still that are pretty good. Here is a link to a decent mid-range one from England. But it’s sort of pricy, and already somewhat dumbed down. Instead, here are some cheaper, more dangerous, American options: 5 experiments you can do (kids and parents together, please) using toxic household chemicals found in our US hardware stores. These are NOT the safest experiments, just cheap ones that are interesting. I’ll also try to give some math and explanations — so you’ll understand what’s happening on a deeper level — and I’ll give some financial motivation — some commercial value.

1) Crystal Drano + aluminum. Crystal Drano is available in the hardware store. It’s mostly lye, sodium hydroxide, one of the strongest bases known to man. It’s a toxic (highly poisonous) chemical used to dissolve hair and fat in a drain. It will also dissolve some metals and it will dissolve you if you get it on yourself (if you do get it on yourself, wash it off fast with lots of water). Drano also contains ammonium nitrate (an explosive) and bits of aluminum. For the most part, the aluminum is there so that the Drano will get hot in the clogged drain (heat helps it dissolve the clog faster). I’ll explain the ammonium nitrate later. For this experiment, you’re going to want to work outside, on a dinner plate on the street. You’ll use additional aluminum (aluminum foil), and you’ll get more heat and fun gases. Fold up a 1 foot square of aluminum foil to 6″ x 4″ say, and put it on the plate (outside). Put an indent in the middle of the foil making a sort of small cup — one that can stand. Into this indent, put a tablespoon or two of water plus a teaspoon of Drano. Wait about 5 minutes, and you will see that the Drano starts smoking and the aluminum foils starts to dissolve. The plate will start to get hot and you will begin to notice a bad smell (ammonia). The aluminum foil will turn black and will continue to dissolve till there is a hole in the middle of the indent. Draino

The main reaction is 2 Al + 3 H2O –> Al2O3 + H2; that is, aluminum plus water gives you aluminum oxide (alumina), and hydrogen. The sodium hydroxide (lye) in the Drano is a catalyst in this reaction, something that is not consumed in this reaction but makes it happen faster than otherwise. The hydrogen you produce here is explosive and valuable (I explain below). But there is another reaction going on too, the one that makes the bad smell. When ammonium nitrate is heated in the presence of sodium hydroxide, it reacts to make ammonia and sodium nitrate. The reaction formula is: NH4-NO3 + NaOH –> NH3 + NaNO3 + H2O. The ammonia produced gives off a smell, something that is important for safety — the smell is a warning — and (I think) helps keep the aluminum gunk from clogging the drain by reacting with the aluminum oxide to form aluminum amine hydroxide Al2O3(NH3)2. It’s a fun experiment to watch, but you can do more if you like. The hydrogen and ammonia are flammable and is useful for other experiments (below). If you collect these gases, you can can make explosions or fill a balloon that will float. Currently the US military, and several manufacturers in Asia are considering using the hydrogen created this way to power motorcycles by way of a fuel cell. There is also the Hindenburg, a zeppelin that went around the world in the 1930s. It was kept aloft by hydrogen. The ammonia you make has value too, though toxic; if bubbled into water, it makes ammonium hydroxide NH3 + H2O –> NH4OH. This is a common cleaning liquid. Just to remind you: you’re supposed to do these experiments outside to dissipate the toxic gases and to avoid an explosion in your house. A parent will come in handy if you get this stuff on your hand or in your eye.

Next experiment: check that iron does not dissolve in Drano, but it does in acid (that’s experiment 5; done with Muriatic acid from the hardware store). Try also copper, and solder (mostly tin, these days). Metals that dissolve well in Drano are near the right of the periodic table, like aluminum. Aluminum is nearly a non-metal, and thus can be expected to have an oxide that reacts with hydroxide. Iron and steel have oxides that are bases themselves, and thus don’t react with lye. This is important as otherwise Drano would destroy your iron drain, not only the hair in it. It’s somewhat hard on copper though, so beware if you’ve a copper drain.

Thought problem: based on the formulas above figure out the right mix of aluminum, NaOH, water and Ammonium nitrate. Answer: note that, for every two atoms of aluminum you dissolve, you’ll need three molecules of water (for the three O atoms), plus at least two molecules of ammonium nitrate (to provide the two NH2 (amine) groups above. You’ll also want at least 2 molecules of NaOH to have enough Na to react with the nitrate groups of the ammonium nitrate. As a first guess, assume that all atoms are the same size. A better way to do this involves molecular weights (formula weights), read a chemistry book, or look on the internet.

Four more experiments can be seen here. This post was getting to be over-long.As with this experiment, wear gloves and eye protection; don’t drink the chemicals, and if you get any chemicals on you, wash them off quick.

Here are a few more experiments in electrochemistry and biology, perhaps I’ll add more. In the meantime, if you or your child are interested in science, I’d suggest you read science books by Mr Wizard, or Isaac Asimov, and that you learn math. Another thought, take out a high school chemistry text-book at the library — preferably an old one with experiments..

Robert Buxbaum, December 29, 2013. If you are interested in weather flow, by the way, here is a bit on why tornadoes and hurricanes lift stuff up, and on how/ why they form. 

My failed process for wood to green gasoline

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Most researchers publish the results of their successful projects, and ignore the rest. It’s an understandable failing given the cost and work to publish and the general sense that the project that flops indicated a loser – researcher. Still, it’s a shame, and I’d like to break from it here to describe a worthwhile project of mine that failed — turning wood into green gasoline. You may come to believe the project worthwhile too, and figure that you might learn from my story some pathways to avoid if you decide to try it. Besides I figure that it’s an interesting tale. All success stories are similar, I find; failure can come in many ways.

Failure can come from incorrect thinking – assumptions that are wrong. One basis of my thinking was the observation that gasoline, for the most part, was crude-oil that had been fluffed up with hydrogen. The density you buy weighs about 5.5 lb/gallon while crude oil weighs 9 lb/gallon. The difference is hydrogen. Perhaps wood too could be turned into gasoline if hydrogen were added. Another insight was that the structure of wood was the structure of a long chain -alcohol,  —(CHOH)-(CHOH)-(CHOH)—. My company had long experience breaking alcohols to make hydrogen. I figured we could do something similar with wood, fluffing up the wood by breaking the long-chain alcohols to short ones.

A possible first reaction step would be to break a C-O-C bond, a ketone bond, with hydrogen:

—(CHOH)-(CH2O)-(CHOH)— + H2 –>  —(CHOH)-CH2OH + CH2OH—

The next reaction step, I imagined was de-oxygenation:

—(CHOH)-CH2OH  +  H2 –>  —(CHOH)-CH3  + H2O

At this point, we are well on the way to making gasoline, or making a gasoline-relevant alcohol like C6H11-OH. The reactions I wanted were exothermic, meaning they would probably “go” — in actuality -∆G is the determinate of reaction favorability, but usually a -∆H and -∆G go together. Of course there are other reactions that I could have worried about –Ones that produce nasty goop. Among these:

–(CHOH)-(CH2O)-(CHOH)—  –> –(CO)-(C)-(CHOH)— + H2O +H2

I didn’t worry about these reactions because I figured I could outrun them using the right combination of a high hydrogen pressure, the right (low) temperature and the right catalyst. I may have been wrong. Then again, perhaps I picked the wrong catalyst – Fe2O3/ rust, or the wrong set of conditions. I picked Fe2O3 because it was cheap and active.

I convinced myself that Fe2O3 was sufficiently specific to get the product to a good 5-6 carbon compounds for gasoline. Wood celluloses are composed of five and six-carbon ring structure, and the cost of wood is very low per energy. What could go wrong? I figured that starting with these 5-6 carbon ring structures, virtually guaranteed getting high octane products. With the low cost and all the heat energy of the wood, wood + H2 seemed like a winning way to store and transport energy. If i got 6 carbon alcohols and similar compounds they’d have high-octane and the right vapor pressures and the products should be soluble in ordinary gasoline.

And the price was right; gasoline was about $3.50/ gallon, while wood was essentially free.  Hydrogen isn’t that expensive, even using electrolysis, and membrane reactors (a major product of our company) had the potential to make it cheaper. Wood + Hydrogen seemed like the cheaper version of syngas: CO +H2, and rust is similar to normal Fischer Tropsch catalyst. My costs would be low, and I’d expected to get better conversion since I should get fewer low molecular weight products like methane, ethane and methanol. Everything fundamental looked like it was in my favor.

With all the fundamentals in place, I figured my only problem would be to design a reasonably cheap reactor. At first I considered a fluidized bed reactor, but decided on a packed bed reactor instead, 8″ long by 3/4″ OD. This was a tube, filled with wood chips and iron oxide as a catalyst. I introduced high pressure hydrogen via a 150 psi hydrogen + 5% He mix. I hoped to see gasoline and water come out the other end. (I had the hydrogen – helium mix left over from a previous experiment, and was paying rental; otherwise I would have used pure hydrogen). I used heat tape and a controller to keep the temperature near-constant.

Controlling the temperature was key, I thought, to my aim of avoiding dehydration and the formation of new carbon-carbon bonds. At too high a temperature, the cellulose molecules would combine and lose water to form a brown high molecular weight tar called bio-oil, as well as methane and char. Bio-oil is formed the same way you form caramel from sugar, and as with sugar, it’s nothing you’d want to put in a car. If I operated at too low a temperature (or with the wrong catalyst) the reaction would be too slow, and the capital costs would be excessive. I could keep the temperature in the right (Goldilocks) temperature, I thought with the right catalyst and the right (high) hydrogen pressure.

No matter how I did this, I knew that I’d get some carbon-carbon bond formation, and perhaps a little char, but so long as it wasn’t too much it should be manageable. I figured I could hydrogenate the tar and remove the char at the end of the process. Most of the gasoline energy would come from the trees, and not the hydrogen, and there would be little hydrogen wasted forming methane. Trees would always be cheap: they grow quickly, and are great at capturing solar energy. Many cities pay for disposal of their tree waste, so perhaps a city would pay us to take their wood chips. With cheap wood, the economics would be good so long as used all the hydrogen I put in, and got some reasonable fraction of energy from the wood. 

i began my reaction at 150°C with 50 psi hydrogen. At these conditions, I saw no reaction; I then raised the temperature to 200°C, then raised the pressure to 100 psi (still nothing) and then tried 250°C, still at 100psi. By now we were producing water but it was impossible to tell if we were hydrogenating the cellulose to gasoline, or dehydrating the cellulose to bio-oil.

As it turned out we were getting something worse that bio-oil: bio-oil gunk. Instead of the nasty brown liquid that’s made when wood is cooked to dehydration (water removal, caramelization), I got something that was nastier than I’d imagined possible. The wood molecules did not form nice chains but combined to form acidic, aromatic gunk (aromatic in both senses: benzine-type molecules and smelly) that still contained unreacted wood as a sort of press-board. The gunk was corrosive and reactive; it probably contained phenol, and seemed bent on reacting to form a phenolic glue. I found the gunk was insoluble in most everything: water, gasoline, oil, methanol (the only exception was ethanol). As best I can tell, you can not react this gunk with hydrogen to make gasoline as it is non-volatile, and almost impossible to get out of my clogged reactor. Perhaps a fluidized bed would be would be better, but I’m afraid it would form wood clumps even there. 

I plan to try again, perhaps using higher pressure hydrogen and perhaps a liquid hydrogen carrier, to get the hydrogen to the core of the wood and speed the catalysis of the desired products. The key is finding a carrier that is not too expensive or that can be easily recovered.

Robert E. Buxbaum, Dec 13, 2013. Here’s something on a visit to my lab, on adding hydrogen to automobile engines, and on the right way to do science. And here’s my calculation for how much wood a woodchuck chucks if a woodchuck could chuck wood, (100 lbs/ night) plus why woodchucks do not chuck wood like beavers.

chemistry and dentistry joke

What do you get when you dissolve all your rear teeth in water.

 

 

An eight molar solution.

 

Is funny because ….. most adults have eight molars (four on the bottom, four on the top); and there is a measure of solution concentration called molarity; an eight molar solution is one that contains 8 formula weights of solute per liter of solution.

For a chemistry joke about dissolving bears, go here; for a chemist v chemical engineer joke, here; for my latest quantum joke, here; and for an architecture joke, here. On a more serious note, if you’d like to see how we do simple electroplating, see the previous post.

 

R.E.Buxbaum, July 24, 2013

Simple electroplating of noble metals

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Electro-coating gold onto a Pd tube by dissolving an iron wire.

Electro-coating gold onto at Pd-coated tube by dissolving an iron wire at REB Research.

Here’s a simple trick for electroplating noble metals: gold, silver, copper, platinum. I learned this trick at Brooklyn Technical High School some years ago, and I still use it at REB Research as part of our process to make hydrogen permeation barriers, and sulfur tolerant permeation membranes.  It’s best used to coat reasonably inactive, small objects,  e.g. to coat copper on a nickel or silver on a penny for a science fair.

As a first step, you make a dilute acidic solution of the desired noble metal. Dissolve a gram or so of copper sulphate, silver nitrate, or gold chloride per 250 ml of water. Make sure the solution is acidic using pH paper, add acid if needed aiming for a pH of 3 to 4. Place some solution into a test tube or beaker of a size that will hold the object you want to coat. As a next step, attach an iron or steel wire to the object, I typically use bailing wire from the hardware store wrapped several times about the top of the object, and run the length of the object; see figure. Place the object into your solution and wait for 5 to 30 minutes. Coating works without the need for any other electric source or any current control.

The iron wire creates the electricity used in electroplating the noble metal. Iron has a higher electro-motive potential than hydrogen and hydrogen has a higher potential than the noble metals. In acid solution, the iron wire dissolves but (it’s hoped) the substrate does not. Each iron atom gives up two electrons, becoming Fe++. Some of these electrons go on to reduce hydrogen ions making H2 (2H+ + 2e– –> H2), but most should go to reduce the noble metal ions in the solution to form a coat of metallic gold, silver, or copper on both the wire and the object. See an example of how I do calculations regarding voltage, electron number, and Gibbs free energy.

Transferring electrons requires you have good electrical contact between the wire and the object. Most of the noble metal coats the object, not the wire since the object is bigger, typically. Thanks to my teachers at Brooklyn Technical High School for teaching me. For a uniform coat, it helps to run the wire down parallel to the entire length of tube; I think this is a capacitance, field effect. For a larger object, you may want several wires if you are plating a larger object. For a thicker coat, I found you are best off making many thin coats and heating them. This reduces tension forces in the coat, I think.

The picture shows a step in the process we use making our sulfur-resistant hydrogen permeation membranes (buy them here), used, e.g. to concentrate impurities in a hydrogen stream for improved gas chromatography. The next step is to dissolve the gold or copper into the palladium.

Go here for a great periodic table cup from REB Research, or for the rest of our REB Research products. I occasionally make silver-coated pennies for schoolchildren, but otherwise use this technology only for in-house production.

R.E. Buxbaum, July 20, 2013.

Thermodynamics of hydrogen generation

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Perhaps the simplest way to make hydrogen is by electrolysis: you run some current through water with a little sulfuric acid or KOH added, and for every two electrons transferred, you get a molecule of hydrogen from one electrode and half a molecule of oxygen from the other.

2 OH- –> 2e- + 1/2 O2 +H2O

2H2O + 2e- –>  H2 + 2OH-

The ratio between amps, seconds and mols of electrons (or hydrogen) is called the Faraday constant, F = 96500; 96500 amp-seconds transfers a mol of electrons. For hydrogen production, you need 2 mols of electrons for each mol of hydrogen, n= 2, so

it = 2F where and i is the current in amps, and t is the time in seconds and n is the number electrons per molecule of desired product. For hydrogen, t = 96500*2/i; in general, t = Fn/i.

96500 is a large number, and it takes a fair amount of time to make any substantial amount of hydrogen by electrolysis. At 1 amp, it takes 96500*2 = 193000 seconds, 2 days, to generate one mol of hydrogen (that’s 2 grams H2 or 22.4 liters, enough to fill a garment bag). We can reduce the time by using a higher current, but there are limits. At 25 amps, the maximum current of you can carry with house wiring it takes 2.14 hours to generate 2 grams. (You’ll have to rectify your electricity to DC or you’ll get a nasty H2 /O2 mix called Brown’s gas, While normal H2 isn’t that dangerous, Browns gas is a mix of H2 and O2 and is quite explosive. Here’s an essay I wrote on separating Browns gas).

Electrolysis takes a fair amount of electric energy too; the minimum energy needed to make hydrogen at a given temperature and pressure is called the reversible energy, or the Gibbs free energy ∆G of the reaction. ∆G = ∆H -T∆S, that is, ∆G equals the heat of hydrogen production ∆H – minus an entropy effect, T∆S. Since energy is the product of voltage current and time, Vit = ∆G, where ∆G is the Gibbs free energy measured in Joules and V,i, and t are measured Volts, Amps, and seconds respectively.

Since it = nF, we can rewrite the relationship as: V =∆G/nF for a process that has no energy losses, a reversible process. This is the form found in most thermodynamics textbooks; the value of V calculated this way is the minimum voltage to generate hydrogen, and the maximum voltage you could get in a fuel cell putting water back together.

To calculate this voltage, and the power requirements to make hydrogen, we use the Gibbs free energy for water formation found in Wikipedia, copied below (in my day, we used the CRC Handbook of Chemistry and Physics or a table in out P-chem book). You’ll notice that there are two different values for ∆G depending on whether the water is a gas or a liquid, and you’ll notice a small zero at the upper right (∆G°). This shows that the values are for an imaginary standard state: 20°C and 1 atm pressure. You can’t get 1 atm steam at 20°C, it’s an extrapolation; behavior at typical temperatures, 40°C and above is similar but not identical. I’ll leave it to a reader to send this voltage as a comment.

Liquid H2O formation ∆G° = -237.14
Gaseous H2O formation ∆G° = -228.61

The reversible voltage for creating liquid water in a reversible fuel cell is found to be -237,140/(2 x 96,500) = -1.23V. We find that 1.23 Volts is about the minimum voltage you need to do electrolysis at 0°C because you need liquid water to carry the current; -1.18 V is about the maximum voltage you can get in a fuel cell because they operate at higher temperature with oxygen pressures significantly below 1 atm. (typically). The minus sign is kept for accounting; it differentiates the power out case (fuel cells) from power in (electrolysis). It is typical to find that fuel cells operate at lower voltages, between about .5V and 1.0V depending on the fuel cell and the power load.

Most electrolysis is done at voltages above about 1.48 V. Just as fuel cells always give off heat (they are exothermic), electrolysis will absorb heat if run reversibly. That is, electrolysis can act as a refrigerator if run reversibly. but electrolysis is not a very good refrigerator (the refrigerator ability is tied up in the entropy term mentioned above). To do electrolysis at reasonably fast rates, people give up on refrigeration (sucking heat from the environment) and provide all the entropy needed for electrolysis in the electricity they supply. This is to say, they operate at V’ were nFV’ ≥ ∆H, the enthalpy of water formation. Since ∆H is greater than ∆G, V’ the voltage for electrolysis is higher than V. Based on the enthalpy of liquid water formation,  −285.8 kJ/mol we find V’ = 1.48 V at zero degrees. The figure below shows that, for any reasonably fast rate of hydrogen production, operation must be at 1.48V or above.

Electrolyzer performance; C-Pt catalyst on a thin, nafion membrane

Electrolyzer performance; C-Pt catalyst on a thin, nafion membrane

If you figure out the energy that this voltage and amperage represents (shown below) you’re likely to come to a conclusion I came to several years ago: that it’s far better to generate large amounts of hydrogen chemically, ideally from membrane reactors like my company makes.

The electric power to make each 2 grams of hydrogen at 1.5 volts is 1.5 V x 193000 Amp-s = 289,500 J = .080 kWh’s, or 0.9¢ at current rates, but filling a car takes 20 kg, or 10,000 times as much. That’s 800 kW-hr, or $90 at current rates. The electricity is twice as expensive as current gasoline and the infrastructure cost is staggering too: a station that fuels ten cars per hour would require 8 MW, far more power than any normal distributor could provide.

By contrast, methanol costs about 2/3 as much as gasoline, and it’s easy to deliver many giga-joules of methanol energy to a gas station by truck. Our company’s membrane reactor hydrogen generators would convert methanol-water to hydrogen efficiently by the reaction CH3OH + H2O –> 3H2 + CO2. This is not to say that electrolysis isn’t worthwhile for lower demand applications: see, e.g.: gas chromatography, and electric generator cooling. Here’s how membrane reactors work.

R. E. Buxbaum July 1, 2013; Those who want to show off, should post the temperature and pressure corrections to my calculations for the reversible voltage of typical fuel cells and electrolysis.