Pique the Geek 20110410: Carbon, the Basis of Life

(9 pm. – promoted by ek hornbeck)

We hear a lot about carbon these days as a greenhouse gas, sort of giving carbon a bad name.  While I agree that excessive carbon dioxide emissions from the wanton burning of fossil fuels is a  bad thing, it is not the fault of the carbon, but rather the fault of civilization for being unwise in how fossil carbon deposits are used.

As a matter of fact, without some carbon dioxide release, we would all starve because atmospheric carbon dioxide is the sole source of carbon in the food chain, thanks to the photosynthetic ability of green plants.  But this topic has been discussed in many places, sometimes in this regular series.  We shall discuss other properties of carbon and why it is essential to life as we understand life, and perhaps all life yet undiscovered.

Of all of the elements, carbon has the most interesting set of properties in its pure form.  There are several allotropic forms of elemental carbon, meaning that they differ only in the way that the carbon atoms are arranged.  The most common form is amorphous carbon, meaning that there is no definite, repeating unit cells which form the basis of crystals.  Amorphous carbon can be in any shape, and is well known with such examples as coal (the Latin name for coal is carbo), charcoal, lampblack, and many other materials.  Some of these are of extreme importance, with coal providing almost half of the United States electricity production.

The two most common crystalline varieties of carbon are graphite and diamond.  One could not even make up how different their properties are.  Graphite is so soft that we use it as pencil “lead” and as a lubricant.  Diamond is one of the, if not the, hardest substance known, used as the ultimate industrial abrasive.  Graphite is a good electrical conductor, for a nonmetal, whilst diamond is an extremely good insulator.  For many materials, thermal and electrical conductivity are related, most good electrical conductors also being good thermal ones.  Carbon is quite the opposite.  Diamond has the highest thermal conductivity of any known substance at normal pressures and temperatures, whislt graphite is such a good thermal insulator that the Space Shuttle uses graphite to insulate its wingtips for atmospheric reentry.  The list goes on, by the way.

Why are those two substances so different when they are made of the exact same atoms?  The answer is how those atoms are attached to each other.  In graphite, the atoms are bonded together in sheets of six membered rings, numbering in the untold billions of these rings fused to each other.  However, it has little three dimensional structure, with the sheets of fused six membered rings attracted to other sheets extremely weakly.  Thus, these sheets are free to slide away from each other, giving graphite its lubricity and softness.  These sheets are also only one atom thick.

In addition, these sheets are formed by two kinds of chemical bonds, sigma bonds and pi bonds.  This comes from the fact that the carbon atoms in graphite are sp² hybrids.  I know that this is a little geeky, but sp² hybrids allow for the delocalization of electrons, making each sheet electrically conductive.  This delocalization also imparts stability, so graphite is more thermodynamically stable than diamond.  Thus, graphite is useful for brushes in electric motors and many other electrical applications.

The case in a diamond is different.  The carbon atoms in diamond are all sp³ hybrizided, thus allowing only for sigma bonds.  Electrons in sigma bonds are not delocalized, so they are not available for electrical conduction.  The atoms in a diamond are arranged in a tetrahedral directions, with each of the four available bonding orbitals 109.5 degrees from the other three.  Thus, each carbon is bonded to four other carbons, forming a rigid three dimensional network.  As a matter of fact, a perfect (no cracks or other flaws) diamond is actually a single molecule!  Who says that molecules are too small to see?  I just gave you an example.

Another unique property of carbon is that it can form long chains of carbon to carbon bonds that are kinetically stable at temperatures up to the ignition point of a material.  Kinetic stability is different than thermodynamic stability, because you can get carbon (even diamonds) to burn, if you heat it hot enough in an atmosphere that supports combustion.  No other nonmetal has this property to any great extent.  This makes life itself possible, because complex chains and rings with carbon backbones are essential for life.  DNA would not be possible without this stability, nor would things like starch and cellulose.  Fatty acids, the essential parts of lipids, would not be stable, nor would proteins which are polymers of amino acids, and the amino acids are composed of chains and rings of carbon atoms.

We hear a lot of speculation about silicon based life forms, with silicon (the element directly under carbon in the periodic table) taking the place of carbon.  However, silicon does not form stable chains.  A carbon carbon single bond has a bond length of 154 picometers and a bond strength of 348 kiloJoules per mole.  The silicon silicon single bond length is 235 pm.  In general, the longer the bond length, the weaker the bond.  In addition, the silicon hydrogen single bond is 148 pm long, whilst the carbon hydrogen single bond is only 111 pm.  One of biggest differences is in the energy released when the oxides are formed.  The enthalpy of formation for carbon dioxide is -394 kJ/mol, whilst for silicon dioxide it is -911 kJ/mol.  This huge difference makes compounds that contain silicon bonded to hydrogen extremely unstable (the negative sign represents that heat is released when the compound is formed from the elements).

This means that compounds of silicon that are otherwise analogous to those of carbon very unstable if oxygen is available.  For example, butane (a four carbon chain with hydrogens everywhere else) has an autoignition temperature (the temperature that is required to ignite in the atmosphere) of 405 degrees C, that of silane (one silicon bonded to four hydrogens) it is less than 21 degrees C, so if you allowed silane to enter the atmosphere at around room temperature, it would burst into flame.  The longer chain ones are even more reactive.

Take a hydrocarbon like methane and bubble it into water, and a little of it (not much) dissolves and the rest just escapes.  Do the same thing with silane, and it explodes!  I just does not seem possible for life to be based on silicon and a drop in replacement for carbon.

On the other hand, it might be possible for large molecules such as are required for life to be based on silicones, polymers with a backbone of silicon oxygen silicon oxygen and so forth.  It might be possible to “hang” sidechains onto this backbone and produce biologically active molecules, but that is a stretch.  Those molecules are less reactive than long carbon chain based ones, and some reactivity is essential for metabolism.  We use silicones all of the time as adhesives, and some of you might even have silicone bakeware.  But I strongly suspect that there are no lifeforms based on silicon in any form.

One of the reasons that carbon behaves so differently than silicon is its position in the periodic table.  With an atomic number of 6, it is in the second row of the table.  Silicon, with an atomic number of 14, is in the third row.  This might not seem significant, but it is critical.  Second row elements have only s and p suborbitals of electrons, whilst third row ones also have d suborbitals.  This greatly changes their chemistry insofar as forming covalent bonds (bonds in which electrons are more or less shared by atoms).  This is much less marked a tendency for ionic bonds (where electrons are more or less transferred from one atom to another).  Thus, carbon and silicon are very different from each other because they form predominately covalent bonds, whilst lithium and sodium are much more similar to each other because they form predominately ionic bonds.

So, I am afraid that the Horta from the original Star Trek episode “The Devil in the Dark” is just not possible.  Remember that one?  McCoy finally healed that silicon based life form with quick setting concrete, a silicate material.

There are other allotropic forms of carbon, such as nanofibers and fullerenes, but they are not that commonly encountered, yet.  They have extremely interesting and potentially useful properties, but are for the most part still in the research phase.  By the way, the carbon fiber that is used as a structural material is not nanofibers, which are formed on the atomic level, but actually just very fine tubes of what is essentially graphite.  These tubes are on the order of a few micrometers in diameter, where actual nanofibers have diameters on the order of one micrometer or less.  The method of production is also quite different.

Carbon forms more compounds than all other elements put together.  Organic chemistry (my academic area) is the study of carbon compounds, although a few, like carbon monoxide, carbon dioxide, and carbonates can be considered to be essentially inorganic molecules.  For a molecule to be an organic one, it must contain carbon, and may contain many other elements.  The most common other elements are hydrogen, oxygen, sulfur, the halogens, nitrogen, and many other are less common.  Phosphorous is a constituent of DNA, as is nitrogen and oxygen.

Sugars are made up of only carbon, hydrogen, and oxygen (although sugar derivatives may have other elements), and thus are called carbohydrates.  Simple sugars can polymerize into starches or into cellulose.  Humans have the ability to digest most of the simpler sugars and starch, but not cellulose.  Ruminant mammals, however, can digest cellulose, making grass and hay valuable foodstuffs for them.  Actually, that is not quite right, it is really bacteria in their complex stomachs that digest the cellulose.  It is the same for termites.

Almost everything that you touch every day has carbon, often lots of it, in them.  The only common examples that come to mind are glass, water, salt, ceramics, and pure metals.  We usually think of steel as being just another name for iron, but this is not the case as all.

Steel is an alloy of iron and carbon!  Pure iron is rather soft and not very useful, whilst steel can be made to be extremely strong.  Sometimes other alloying materials are added to specific grades of steel, but without carbon it is not really steel, but some other ferrous alloy.  Pure iron also can not be hardened by heat treatment, but steel can be.  Up to a point, the higher the carbon content, the greater the hardenability.  A little carbon goes a long way:  high carbon steels contain only about one per cent carbon.

There are three naturally occurring carbon.  Carbon-12, the most common isotope, with 6 neutrons in addition the the 6 protons, amounts to 98.9% of it, and carbon-13, with 7 neutrons, about 1.1%.  Both are stable and do not decay into other materials.  Carbon-13 is of particular interest to us organic chemists because it happens to be a nucleus with a spin=1/2, essential for nuclear magnetic resonance spectrometry.  With NMR, how atoms are connected in molecules can be elucidated, and since carbon is a constituent of all organic compounds this is a stroke of luck.  By the way, there is another nucleus with spin=1/2, the hydrogen nucleus.  This makes hydrogen NMR possible, and also Magnetic Resonance Imaging (MRI), that is used as a medical diagnostic tool.

Carbon-14 is a radioactive isotope that is formed in the atmosphere by cosmic ray bombardment of nitrogen-14.  The nitrogen molecule immediately dissociates, and the carbon-14 atom immediately reacts with atmospheric oxygen to for carbon dioxide.  This radioactive carbon dioxide is taken up by plants and thus enters the food chain.  It has a half life of 5730 years and decays by the relatively harmless and easy to measure soft beta decay.  When a plant dies (or an animal, for that matter, since all animal food is ultimately derived from plants) the steady state concentration of carbon-14 begins to become smaller, by a known rate.  In other words, all living things contain about the same amount of carbon-14 because it is constantly being replenished.  When an organism dies, it stops taking in new carbon-14, and what is there decays.  If something has been dead for 5730 years, only half of the radiation that a living specimen is present.  In another 5730 years, only 1/4 of the radiation is left, and so on.  Modern instrumentation is so sensitive that only a few milligrams of sample are required for analysis.  It good for items up to around 60,000 years, when the amount of radiation becomes too low for accurate measurement.  There are some nuances involved, but that is the general principle.  Ask in a comment if you would like more information.

Carbon-12 is the forth most abundant element in the known universe, after hydrogen, helium, and oxygen.  It is formed in stars of high mass that are beginning to collapse because of depletion of hydrogen for fuel.  When this happens, the core becomes extremely hot and dense, and two helium nuclei fuse to form beryllium-8.  This extremely unstable nucleus sometimes fuses with another helium nucleus to form carbon-12, which is stable.  Carbon should be more abundant than oxygen, but sometimes a carbon-12 nucleus absorbs another helium nucleus to form oxygen-16, depleting the amount of carbon-12.

Well, this is long enough.  Since I always learn more than I ever could hope to teach by writing this series, please keep comments, questions, corrections, and any other feedback coming in the comment section, the best part of the post.  I shall stick around as long as comments warrant, and will return tomorrow night for Review Time around 9:00 PM Eastern.

I must comment of the latest foolish thing that Isadore Rosenfeld said on his weekly medical piece this morning on the Fox “News” Channel.  Whilst extolling the virtues of breastfeeding (with which I fully concur), he said this, and I believe that this is verbatim:

Everything that is natural is good.

I disagree.  Anthrax is natural, and no one says that it is good.  Ebola is natural, but I do not think that it is good, either.  Floods, earthquakes, tornadoes, tsunamis, hurricanes, and other such are natural, but few would agree that all of them are good.  This guy needs to retire.

Warmest regards,

Doc