This is one in the series of the ETFRC's "backward chaining" learning essays, intended to serve only as a rapid introduction to a particular subject, so that lack of familiarity with the subject doesn't block one from learning something else.  What is discussed here is only the briefest sketch of the chemistry of carbon, but we hope the information is detailed enough that the topic, in this case organic chemistry, doesn't become a stumbling block that stops the reader from learning what led him or her here.  Each of these essays provides a link to a far more in-depth book on the subject.  It is our hope that readers will want to continue their study at greater depth, for each of these topics is itself intrinsically interesting.

We can say that the universe consists of a substance, and this substance
we will call "atoms," or else we will call it "monads." Democritus called it atoms.
Leibniz called it monads. Fortunately, the two men never met, or there would
have been a very dull argument.

Woody Allen, My Philosophy

What's Reality Made Of?

Chemistry is a really broad topic.  The best way to think of it is as an answer to the question, "So, what's the world made out of, anyway?" and that's the question we're going to approach in this little essay.   What is the world made of?  What are stars, planets, vegetables, and animals made of?  What's actually here?

Well, first, let's list the things we're not going to be discussing.  Obviously, there's lots of energy in the universe, but this factors into chemistry only in a tangential way, so for the most part, we won't be talking about energy.  The universe also at least seems to have, or be, or contain, or something, phenomena like space, time, and consciousness.   These are surely fascinating phenomena, but right now we're going to be discussing things much closer at hand, and less philosophical.  For this essay, we really want to focus on the "stuff" that the world is made of.  What is this stuff?

At the most fundamental level (chemically speaking; physics goes far deeper than this), the universe is made of atoms.  Atoms (again, from a chemical perspective) can be thought of as being made from very primitive bits of matter, subatomic particles, called protons, neutrons, and electrons.   As far as the question of what these things are goes, my best understanding is that no one really knows.  Explanations have to stop somewhere, and if we keep pressing the quesiton, "Yeah, but what is matter?" we're in grave danger of finding ourselves philosophizing.  Really smart people have come up with a way of describing the subatomic world called quantum mechanics (QM).  But there are several "interpretations" of the meaning of QM, and no one seems to know which, if any, of them is the "right" one, or if all of them are "right," or what it means for an interpretation of something to be "right," or something, or nothing.  This doesn't mean that QM is some kind of shaky theory; on the contrary, the predictions it makes for chemistry have been so thoroughly verified that we're entirely justified in regarding it as being far more than a mere "theory."  But the overall view of reality that the elaboration of QM gives can be understood in several different ways, and all of them are very strange and show a reality vastly weirder than anyone pre-QM could have imagined.   This brief sketch of chemistry can't possibly discuss QM, and won't try, except to point out where old ideas have to be discarded to have even a minimal grasp of what's going on.

There is no way to talk about chemistry without talking about protons, neutrons, and electrons, and a tiny bit of QM goes a long way toward helping us understand why molecules are shaped as they are, but really, we can entirely dispense with the quantum stuff and still get a pretty good picture of what's going on.  Such a view is usually called "classical" chemistry.  QM entirely changes our ideas about what subatomic particles are, but the molecular level is just barely large enough that we can envision it adequately with classical ideas, and not much of the picture will be lost.  Keep in mind that, once you're into a certain topic, you can always learn more about it, but if you get bogged down right from the start, you're unlikely to ever find it interesting.

Atoms and Elements

So, let's talk about atoms.  There is a finite and fixed number of kinds of atoms, based on the number of protons that the atom has.  These kinds of atoms are called elements, and a very famous chart called the periodic table of the elements lists them all and shows how they naturally fall together into families.  The simplest possible element, and the most plentiful one in the universe, is hydrogen, which consists of one proton, one neutron, and one electron.  Most people, to the extent that they think about the subject at all, think of electrons as tiny balls "orbiting" the proton-neutron nucleus of the atom at a great speed.  Thanks to QM, we know that this picture of the electron is completely wrong.  The understanding that QM gives, of course, verges on the Mystical and Ineffable, but it's sufficient for us to think of the electron in a hydrogen atom as a cloud around the nucleus, which thins out the further away from the nucleus it gets.  Although we won't be delving into QM, any "billiard ball" ideas anyone has about atoms should be jettisoned right now.  Atoms are not like planets in their orbits around the sun, or anything like that.  They're much vaguer than that; they can be thought of as being fuzzy and blurry things that are denser in some places than others. 

After hydrogen, subsequent elements have an additional proton, neutron, and electron -- helium has two, lithium has three, beryllium has four, and so on.  This number is called the atomic number of the element.  There are 92 elements that occur in nature -- from hydrogen to uranium -- and a bunch of entirely synthetic elements which are called transuranium elements.   These are created using tremendous energies in particle accelerators, and are of absolutely no interest from the perspective of organic chemistry.  The 92 natural elements are the whole pallet from which reality is painted.  That's it.   Everything in the universe is made of some combination of these 92 things.    And in fact, just four elements account for almost everything we'll deal with in organic chemistry.  Those four are: carbon, hydrogen, oxygen, and nitrogen.  Sure, sulfur, chlorine, flourine, phosphorous, iodine, and others occassionally make an appearance, but it really is staggering to realize that, for starters, 99% of the entire living world is made up of these four elements.  Organic chemistry was originally given its name because it was thought of as the chemistry of living things, as opposed to, say, rocks, which have a very different kind of chemistry.  But today it is properly understood that organic chemistry is the chemistry of carbon, the sixth element, which has certain unique properties that allow endless elaborate structures to be created from it.  Life -- proteins, carbohydrates, fats, nucleic acids, steroids, and so on -- as well as drugs, plastics, fossil fuels, and many other things are built on this astounding foundation.

Just as in the macro world that we see and live in, the shape of things is very important in the chemical world.  The most straightforward way to think about molecular geometry is that all of the groups bound to a central atom will arrange themselves so as to be as far apart from one another as possible, like people getting into an elevator.  This is the most "relaxed" shape -- that is, the lowest energy shape -- that the molecule can assume, and molecules always want to be as relaxed as possible.  It's really helpful to have a molecular modeling kit, like the one from Prentice-Hall which we provide a link to at the top of the page, when learning chemistry.  Most molecular modeling kits are pretty much equally servicable.  Much more important than which one you get is that you get one.  One really cannot overstate how useful they are in learning to mentally envision molecules.

Molecules and Bonds

So what is a "molecule," anyway?  A molecule is simply two or more atoms, joined together and arranged in a particular way.  The joining and arrangement of the atoms (which is called synthesis) makes a new thing, a chemical that is an entirely different thing from the elements or compounds that it was built from.  A molecule of something is the smallest bit it can be divided into and still remain what it is.  Water, H₂O, has properties very different from those of the hydrogen and oxygen that it's built out of.  This is very important to understand, and that's why I'm saying it over and over.  When a chemical reaction occurs, the resulting molecule is not a mixture of the reactants, it is a brand new thing that may have no relationship at all, in terms of its properties and behavior, to the things it was synthesized from.  Organic chemistry is about molecules, specifically, molecules based on carbon.

The two most common means for atoms to associate into molecules are called bonds -- the ionic bond, and the covalent bond.  In an ionic bond, the molecule is held together by equal and opposite electrical charges.  This kind of bond is most frequently seen in inorganic chemistry.  For example, ordinary table salt is sodium chloride (NaCl), and we can see from the periodic table that Na and Cl have equal and opposite charges, with Na⁺ being the positively charged sodium ion, and Cl^- being the negatively charged chlorine ion.  We see that Na, element 11, is in group I-A of the periodic table.  With the exception of hydrogen, which lives in its own world, all of the elements in group I-A have a +1 positive charge.  Chlorine (Cl), on the other hand, element 17, is in group VII-A.  The members of this column are called the halogens, and they all have a negative charge of -1.  The halogens tend to attract electrons, while sodium and its cousins in the periodic table tend to supply electrons.   Column 18, which is group VIII-A,  is made up of the "noble gases" or "inert elements" which have no net charge and tend very strongly not to enter into reactions or become part of molecules.  It turns out that these numbers, one through eight, are very important in chemistry.  Never forget that the periodic table is not merely a list of the elements, but its arrangement depicts the increase and decrease of various properties of the elements.  One such property, electronegativity, which is the tendancy to attract or supply electrons mentioned above,  increases as one moves from the left-hand side of the table to the right, and suddenly disappears in the rightmost column.

What does it mean to say that an atom has a "charge" of   "+1" or "-1."  Charge is a property carried by electrons -- that's how they originally got their name -- and something has a charge of +1 if it has an electron available to share.  A charge of -1 means that the atom is one electron shy of being stable and wants to attract an electron from somewhere.  The distribution of electrons into orbitals (or shells, in classical terms) of varying degrees of stability is a complex topic, and here will will cop out and explain it away in the simplest possible terms: one can picture the electrons of an atom arranged into shells which, when full, hold eight electrons, except for the first, or innermost, shell, which holds two.  The outermost shell of an atom holds what are called the valence electrons; it is these which become involved in reactions and bonding.  The old-style group numbers, which are shown in the periodic table above, are identical with the number of valence electrons the atom has.  An atom is maximally stable when its valence shell contains eight electrons (the "octet rule," in pre-QM terminology), as can be seen looking at group VIII-A, the non-reactive "noble gasses," which are perfectly stable and tend to neither gain nor lose electrons.

Above we mentioned that inorganic compounds, such as salts, are often formed by ionic bonds, in which the atoms thus bound are held together by electrostatic attraction due to their equal and opposite charges.  When such a compound is dissolved, as when NaCl is dissolved in water, it immediately dissociates into its constituient ions.  In the case of NaCl, this means that, in solution, it becomes Na⁺ and Cl^-.  The resulting solution will conduct electricty, since it contains ions.  The ionic bond which gives NaCl its crystalline geometry in the solid state has essentially been lost once the compound is dissolved.  Unlike NaCl, lots of compounds, for example, alcohol, can be dissolved in water, but the resulting solution will not carry an electrical current, indicating that alcohol is not an ionic compound.  We know that alcohol (let's talk about ethyl alcohol, also called ethanol, and othewise known by the technical terms booze and hooch) is made of atoms that we can write as CH₃CH₂OH, where C is the periodic table's symbol for carbon, H is the symbol for hydrogen, and O is the symbol for oxygen (this form of description of a molecule, which tells us how many of which atoms are in it, is called its empirical formula).   We know that a solution of ethanol doesn't conduct electricity, indicating that the atoms haven't dissociated into ions.  They aren't held together by electrostatic attraction.  So what does hold them together?  It wasn't until 1916 that the American chemist G. N. Lewis proposed an electrical model for non-ionic bonding of atoms.  Lewis' idea was that the atoms were held together by shared electrons.   This kind of bond, called a covalent bond, is what holds organic compounds together, and determines a good deal about their basic shape and their ability to assume other shapes.

Okay, now that we're clear on all of that stuff, it's time for the inevitable organic chemistry question, "What's so special about carbon, anyway?"   That's what you were just now thinking, isn't it?  I knew it.  Of the approximately twenty million chemical compounds known, more than 80% of them are organic (i.e., they are carbon-based).  Carbon has several special qualities that allow a virtually infinite number of stable structures to be based on it.  The most important of these qualities is that carbon can covalently bond to itself, something which is true of very few elements.  It also forms strong covalent bonds with hydrogen, nitrogen, and oxygen, as mentioned above, and with the other elements discussed above which are less common in organic structures than the Big Four.   If that's not enough, carbon's covalent bonds can be single, double, or triple, based on the number of electron pairs shared.  As a tetravalent atom, carbon sits right in the middle of the magic number, eight, that makes up a full "electron shell."  This means it can have four covalent bonds.  The ability of carbon to bind to itself means that organic compounds can range in size from tiny to enormous.  Its self-binding property means that organic compounds can take the form of straight lines of carbon, branched structures of every kind, and rings, or cyclic compounds made up of various numbers of carbon atoms, or cyclic compounds made up of carbon and other elements. Cyclic structures can share bonds and thus be fused to make up heterocyclic structures.   The possibilities are almost literally endless.

Types of Organic Molecules

The figure above depicts methane, CH₄, the simplest organic compound, and shows the general shape of carbon compounds: the four bonds are arranged in three-dimensional space like a tetrahedron.  Figure (a) is a standard structural formula, which you will see constantly if you study organic chemistry.  Unlike an empirical formula, a structural formula shows not only which atoms make up the compound, but how they are arranged as well.  Figure (b) is a three-dimensional variant of the structural formula, which makes methane's tetrahedryl shape clear.   It's important to remember that organic compounds exist in space; they are not flat like drawings of their structural formulae.  As one learns more, and especially if one fiddles around with a molecular modeling kit, one's ability to visualize the three-dimensional shape of a molecule given the flat structural formula increases.   Finally, figure (c) is a space filling model of methane, which shows not only composition and arrangement, but also the relative size of the atoms involved.   This is the way we want to picture molecules in our minds, but for notation, structural formulae have the great advantage of having nothing hidden in the drawing.   When a space filling model is rendered on paper, it must be drawn from some particular vantage point, and, from that vantage point, parts of the molecule may be obscured.

Because of the great variety of structures that carbon atoms can form, organic compounds encompass an enormous range of shapes and sizes.  To handle this complexity, organic chemistry has evolved an extremely systematic way of drawing and naming compounds, such that one can draw the molecule knowing only the name, and one can produce the name from only seeing a picture of the molecule.  The language of chemistry relies on breaking the molecule down into its component parts, which all have names.  To begin our study, then, we're going to look at the various fundamental arrangements of carbon atoms, and the name of each type.

The simplest organic compounds are called hydrocarbons, because they contain nothing but hydrogen and carbon atoms.  Yet, even limited to these two atoms, carbon can produce an almost endless variety of structures.  To get a handle on this, hydrocarbons are broken down into four types.

In the fourth type of hydrocarbon arrangement, the behavior of the participating electrons becomes a bit stranger.  These structures are said to be resonant (the older term for them was aromatic) because of the way their electrons distribute themselves among the molecule's atoms.  The prototypical armoatic hydrocarbon is the cyclic compound called benzene.

Benzene
Double/Single Bond Arrangement in Resonance

In this picture, the idea is that the position of the double bonds in the ring can be seen as rapidly shifting between two equivalent states, but that isn't the ideal way to picture resonance.  Another way to depict benzene is by drawing a cyclohexane ring with a circle in the middle of it, rather than alternating single and double bonds.

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