Sep 10 2012

Pique the Geek 20120909: Oxygen Wrapup

Last time we discussed oxygen as an element, including why we do not burst into flame in our 21% oxygen atmosphere.  Quantum mechanics can really be interesting.

This time we shall discuss some of the compounds of oxygen with other elements, and I emphasize SOME because oxygen forms hundreds of thousands if not millions of compounds.

Some of these compounds are essential industrial materials, some are essential for biological processes, and some of them can cause real problems when released into the atmosphere.  A few of them are quite toxic.  Let us look into them!

One of the simplest oxygen compounds is carbon monoxide, CO.  Carbon monoxide has the same number of electrons as N2, and we would expect a triple bond in this case.  Sure enough, a structure with triple bond can be drawn and it turns out that this triple bond is even stronger than the nitrogen triple bond, being the strongest chemical bond thus discovered.  The Lewis dot structure can be represented by three resonance forms, and each of them have a bit of a problem.  Here they are:


The first structure gives each atom an octet of electrons, and that is a very good thing.  However, it also places a formal positive charge on oxygen, the second most electronegative element and a negative charge on carbon.  From electronegativity aspects alone we might conclude that this is not a very good structure.  We would be quite wrong.  In the middle structure we pushed two electrons from the triple bond onto the oxygen.  No atom has any charge now, which is a good thing, but now carbon has only six electrons around it, so it does not have an octet.  That is a bad thing.  The right structure is even worse, because carbon has only four electrons.  The charges make sense, with the negative charge on the oxygen and the positive one on the carbon.  However, the octet rule is much more important than formal charge and the left hand structure contributes more than the others to the actual distribution of electron density.  Indeed, studies show that carbon monoxide DOES have a positive and a negative end, and the positive end is the oxygen end!

There is something else a little screwy about CO.  Remember, carbon has four valence electrons and oxygen has six.  That means that one of the triple bonds in the left structure come solely from oxygen, since carbon just does not have enough to contribute.  These are called dative bonds and I shall not ever mention them again.

We all know that carbon monoxide is quite toxic, but that does not mean that it is not of use for good as well.  The reason that it is toxic is that it displaces oxygen from hemoglobin and renders hemoglobin incapable of allowing respiration.  In addition, the carbon monoxide/hemoglobin combination is more stable than the oxygen/hemoglobin one, so that complex is hard to break up once it forms.  In fact, in normal air the half life of the complex is over five hours.  Thus, relatively low concentrations of CO can be quite dangerous over the long term, since it builds up in the body.  Treatment is oxygen or pressurized oxygen, all to speed the process of breaking the carbon monoxide/hemoglobin complex.

Carbon monoxide also binds to myoglobin, the primary protein in muscle.  Myoglobin also contains iron.  Myoglobin bound to oxygen is bright red, but oxidation changes that red color to brown as the iron goes from the 2+ oxidation state to the 3+ one.  However, if the air in a package of meat is replaced by carbon monoxide, the CO/myoglobin complex (around 60 times more stable than the oxygen complex) keeps the iron in the 2+ state and the meat stays nice and red.  Most people do not know that this is commonly done in the retail meat trade.  Hold your CO detector against a small hole in the plastic film and see if it responds.  It is not harmful to eat such meat, and the CO does not penetrate that deeply anyway.

There are lots of uses for CO, some of them as a fuel since it burns to carbon dioxide with release of heat.  Several industrial processes exist that make CO from coal or coke and air or water.  These gases are used industrially for combustion to provide heat for various processes.

Generally when we burn a fuel we want all of its fuel value to be released for economic reasons.  When I was designing smoke grenades for the Army, it is undesirable to burn the fuel (in our case, powdered sugar) all the way to carbon dioxide, because it releases too much heat and burns up the smoke (actually organic solids aerosolized by the combustion).  We want to make the smoke material hot enough to become small particles, but not hot enough to burn them up or to char them.  The solution was to add just enough oxidizer (in my case, potassium chlorate) to burn the the sugar to CO and water, not CO2 and water, producing a cooler flame. The enthalpy of formation for carbon monoxide is -110.5 kJ/mol whereas that for carbon dioxide is -393.5 kJ/mol, so much less heat is released when carbon in burnt only to carbon monoxide.

We also hear of carbon dioxide all of the time.  Carbon dioxide is essential for life, as all of the food that exists ultimately is derived from it.  Indeed, carbon dioxide is the source of all of the carbon in us, yet we exhale it as a waste product!

Carbon dioxide can be represented by a single, linear structure:


All atoms have an octet of electrons and there is no charge to be placed on any atom.  This is a stable configuration.

Most carbon dioxide is trapped as carbonate rocks, many of which formed during the Carboniferous Period when atmospheric carbon dioxide levels were high.  We think that carbon dioxide levels in the present atmosphere are high (and they are compared to the preindustrialized planet), but everything is relative.  Even though the current level is around 390 parts per million (0.039%), it is very tiny.  For example, what we think of as the very rare gas neon occurs at about 15 ppm.  By the way, the preindustrial level was around 250 ppm.  All units are in volume to volume.

Carbon dioxide is constantly being produced by the respiration of animals, but by many other things as well.  Volcanoes are rich in carbon dioxide in many cases, and acid rain releases it from carbonate rock.  Increasingly as fossil fuels are burnt, carbon dioxide is being added to the atmosphere faster than the oceans can convert it to carbonate and plants can use it.  This leads to global climate change and that is not the topic tonight.

Carbon dioxide has lots of uses, in industry, in consumer affairs, in medicine, and in chemistry.  This is one gas that everyone in the developed world has seen, since it is what makes soda, beer, and champagne fizz.  One of my favorite chemists, Joseph Priestly, was the first to add carbon dioxide to water artificially, producing what we call Seltzer, carbonated water, or sparkling water in 1772!

Carbon dioxide is extensively used as a fire suppressant because it is already burnt, is nontoxic, does not leave a residue, and is cheap.  It is not good for electronics because when it reacts with water (remember, water is almost always produced in a fire), it reacts to form carbonic acid, and that can be corrosive until the carbon dioxide evaporates.  The carbonic acid is responsible for the sour taste of carbonated water.

Carbon dioxide can not exist as a liquid at ambient pressure.  It can be liquefied easily with pressure, and both fire extinguishers and the bottles used in soda fountains are pressure vessels that contain liquid carbon dioxide inside.  When the valve is opened, the liquid boils off gaseous carbon dioxide.  In soda fountains the goal is to get the gas, but in fire extinguishers the goal is to throw the liquid out, which instantly becomes a solid (a very cold solid) at atmospheric pressure.  Thus, in a soda fountain the gas at the top of the vessel is tapped, whilst in a fire extinguisher the liquid from the bottom of the vessel is discharged.

A very interesting form of carbon dioxide is dry ice, simply solid carbon dioxide.  It is made sort of using the fire extinguisher principle, allowing liquid carbon dioxide to be discharged in a catch vessel at atmospheric pressure.  The carbon dioxide “snow” that results is then pressed into more dense forms.  Dry ice is used for refrigeration purposes in every niche of the economy just about.  Physics teachers use “pucks” made of it to demonstrate the effects of friction (the gas subliming from the bottom of the disc makes an almost frictionless contact on a smooth table).  It can be used for mischievous purposes as well.  A 2 liter plastic soda bottle with a little water in it becomes very loud a few minutes after some dry ice is added.  The dry ice sublimes, taking the pressure beyond the failure point of the soda bottle.  Soda bottles do not start leaking; then fail catastrophically.  The result is a huge bang but little collateral damage since the soda bottle pieces have little momentum and catch a lot of air.  Do not try this at home, because I understand that some jurisdictions have designated these toys as destructive devices, and I would hate for anyone to get a felony rap for something as silly as this.

As a public service I found a video of one.  The report is quite remarkable.  Watch it so you do not do this yourself!

When I was a postdoctoral fellow at The Georgia Institute of Technology a friend of mine, a graduate student, set one off on the roof of the chemistry building.  He was back in the laboratory before it did its thing, and it was amusing to watch the campus police come and look for what happened.  Since the dry ice all sublimed before they got there, all that they could find was a wet place and pieces of old drink bottles.

Carbon dioxide is used in medicine to stimulate respiration.  It turns out it is not lack of oxygen that makes you want to gasp for air.  It is the buildup of carbon dioxide that causes the panic.  Typically, 5% in oxygen is given to patients requiring oxygen and in need of respiratory stimulation.  I saw on TeeVee many years ago a guy breathing in a closed system.  After a while the carbon dioxide levels got so high that he tore off the mask.  Next he inserted a sodium hydroxide cartridge in the tube after the closed system had been flushed with fresh air.  After he put on the mask, he just kept on breathing until he passed out, never feeling any panic.  The medical team standing by got him out of the mask and he came back around.  By the way, sodium hydroxide absorbs carbon dioxide but leaves the other gases (except for water vapor) alone.  The guy simply used so much of the oxygen in the system than the atmosphere would no longer support life, and it did not bother him.

One of the most common compounds of oxygen is the one with silicon, silicon dioxide, SiO2.  In crystal form it is called quartz, among other crystal forms.  Enormous amounts of silicon dioxide in the form of white sand is used in making all kinds of glass, and this in an ancient use.  Interestingly, this ancient material is also critical to the electronics age because of the piezoelectricity that it demonstrates.  Basically, when a crystal is deformed (but not enough to break it), an electrical charge is produced.  Likewise, when an alternating electrical charge is impressed onto the crystal, it changes shape in a periodic manner, called oscillation.  Quartz watches keep time using a crystal to regulate the clock cycle, and this use is found in very many electronic devices.  You may have seen those cigarette lighters the shoot a little spark when the trigger is pressed rather than using a flint.  The piezoelectric element in those is not quartz, but a ceramic tailored for that purpose.

Silicon dioxide is also used to make glass that resists thermal shock.  The Corning product Vycor can be frozen into a block of ice and molten lead poured onto it without breaking.  Pure silicon dioxide is even more shock resistant, but is hard to work because, being a pure substance, has a sharp melting point rather than a softening range.  When I was a graduate student I used a lot of fused silica apparatus because, unlike glass, fused silica is transparent to ultraviolet light down to around 165 nanometers or so, where Pyrex cuts off at at around 280 nm.  Pyrex was actually perfect for some of my work, when I was using the 313 resonance mercury line, but if I needed the 254 nm line, I had to use quartz.

Oxygen forms compounds with almost all other elements, and some oxides are important ores.  Oxides of iron have been used since antiquity as iron ores, and the final products from iron refining are basically metallic iron and carbon dioxide.  By the way, steel production is a large contributor of carbon dioxide into the atmosphere.

Bauxite, the ore of aluminum, is a hydrated aluminum oxide.  Cassiterite, the ore of tin, is tin dioxide.  Pyrolusite, the ore of manganese, is manganese dioxide.  Ilmenite, the ore of titanium, is a double oxide of iron and titanium.

Of course, water is the most immediately important compound of oxygen for us living things.  I wrote about water before, and if I have time I shall look for the link.  I am running a little late tonight.

I mentioned that oxygen is extremely important in biological systems, and it is.  Every major biological molecule, with extremely few exceptions, contain oxygen.  Sugars are compounds of carbon, hydrogen, and oxygen and are made from carbon dioxide from the atmosphere and water from the sea or ground by green plants in that magic process of photosynthesis.  It takes six molecules of carbon dioxide to make one molecule of glucose, the basic building block that creates the rest of the carbohydrates.  Carbohydrates can be simple molecules like glucose to polymers of up to 10,000 glucose units, called cellulose.  Cotton is one of the 10,000 ones and that is why it makes better paper than wood pulp, only around a couple of hundred glucose units long.

Oxygen is also a key constituent of amino acids, the building blocks of proteins.  Here is a generic structural formula for an amino acid:


The group in green is the acid part of the molecule, and is present in all amino acids.  Without oxygen, life could be possible, at least as we understand life.  Even your DNA contains oxygen, because the sugars in it all contain oxygen.

Fats all have oxygen in them, because they are derivatives of fatty acids and glycerol, both of which contain oxygen.  Here is a different kind of structural formula for a fat.  The black spheres are carbon atoms, the white ones hydrogen, and the red ones oxygen.

Most of our recreational molecules contain oxygen.  The most widely used one, alcohol, does.  So does THC.  As does caffeine.  Nicotine does not, but it has a nitrogen (someday I will get into the importance of nitrogen for psychoactive materials).

Some of the most useful materials that we have for making things contain oxygen.  I already mentioned glass, which always contains oxygen in some form.  Other examples include nylon, which is almost like a protein in that it is made of long chains of smaller molecules that contain both nitrogen and oxygen.  Cellulose, in the form of wood (actually a wondrously complex natural composite material of cellulose and lignin) builds our houses.  In the form of paper, cellulose allows us to communicate across the ages.  In the form of cotton, it clothes us.

I strongly suspect that everyone reading this is using oxygen even now.  That is because biological processes require that glucose be burnt by oxygen to carbon dioxide and water, releasing energy.  One might imagine that glucose to be the gold reserve that once backed most currencies.  The dollars in this economy are adenosine triphosphate, or ATP.  Itself based on a sugar, it is extremely oxygen rich, viz.:


Glucose itself is not as well fitted to enter into actual reactions, so most biological systems use glucose burning to make ATP, and the energy contained in the ATP in turn enters into thousands of reactions to release energy.

Well, I am starting to ramble and it is almost post time.  Please let me know if I should do one more installment about oxygen or move to the next element.

Well, you have done it again!  You have wasted many more einsteins of perfectly good photons reading this flammable piece.  And even though Chuck Norris realizes that his silly attempts at jokes on the Huckabee show tonight just make him look small when he reads me say it, I always learn much more than I could ever hope to teach by writing this series.  Thus, please keep those comments, questions, corrections, and other feedback coming.  Tips and recs are also always welcome.  Remember, no science or technology issue is off topic here.

I shall remain for Comment Time as long as traffic warrants.  I have no one to visit in person tonight, so I visiting with my friends here will be an honor.  I shall return tomorrow evening around 9:00 Eastern for Review Time.

Warmest regards,

Doc, aka Dr. David W. Smith

Crossposted at

Daily Kos,

Docudharma, and


1 comment

  1. Translator, aka Dr. David W. Smith

    an amazing element?

    Warmest regards,


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