Compounds of carbon: organic chemistry

In this section, we begin a study of organic chemistry, the chemistry of carbon, upon which life on Earth is based. A vast number of compounds and their reactions, both in living and non-living systems, are based on carbon as a "backbone" atom.

Even the chemistry of nonliving carbon-based things, by the way, usually traces its origins to once-living things. For example, we make a great many plastics and other kinds of polymers from oil byproducts, and oil is the remains of dinosaurs and other animals long extinct.

Alkanes – the simplest hydrocarbons

Alkanes are hydrocarbon compounds that contain only single (sigma, σ) bonds between carbon atoms. The simplest possible alkane consists of just one carbon atom bonded to four hydrogens, methane, CH₄

Now we need to take a moment here and think about the kinds of drawings we'll be making. The methane structure above isn't much of a 3-D rendering of the actual structure of methane. We know, in fact, that methane is tetrahedral, and looks more like this:

In the notes that follow, we'll mostly ignore 3D information and draw flat structures. In fact, we'll strip a way most of the detail a little later to make some bare-bones (but more convenient) drawings. Still, you should always be mindful that these flat, "chemistry on paper" structures stand for three-dimensional things.

The next larger alkane is ethane, C₂H₆, shown here:

Ethane begins a series of hydrocarbon molecules that we call "normal" hydrocarbons (often signified by the letter n), or "straight-chain" hydrocarbons. The next in the series is propane, or n-propane

You may be getting the idea by now. The alkanes are named by appending the suffix "ane" to some prefix that matches the number of carbons in the chain. So far we've used prefixes "meth" to signify one carbon, and "eth," to signify two."

Prefixes and suffixes, naming of compounds and deducing the chemical bonding from a name will be important in organic chemistry. This is foundation stuff that you just have to know. Take the time to learn it, but also realize that learning will come from reading further and recognizing patterns.

Remember, more things are similar in chemistry than different. Look for those similarities and exploit them to learn.

Structural isomers – different ways of arranging the same alkane.

For alkanes with more than three carbon atoms, it turns out that there can be more than one – often several – ways of bonding the same set of carbon and hydrogen atoms. These compounds are called structural isomers (iso = "same", mer = "thing"). For example, let's take a look at two structural isomers of butane, called n-butane for normal butane, and isobutane, for a branched form with the identical molecular formula, C₄H₁₀.

Make sure to count the carbons and hydrogens; they're the same. The thing is, these two compounds have different chemical and physical properties and different uses, so we'll need a way to name them to tell them apart.

Straight-chain alkanes

We generally refer to straight-chain alkanes with the designation n for normal. Here we've called the C-C-C-C version of butane n-butane. That's common. If we refer to n-hexane, we mean C₆H₁₄ with all carbon atoms arranged in a line.

Naming branched alkanes

Now we can also arrange any alkane longer than propane with some of its carbons (with its compliment of hydrogens) branching off from a main chain. While some of these molecules have special names that we have inherited from the beginning days of chemistry, like isobutane in this case, there is a standard way of naming them.

We begin by labeling the carbon atoms of the main (longest) chain from 1 to however many there are. Don't worry about where to begin just now, we'll tackle that later. Roll over the figure below to see how the branched form of butane is labeled.

Example 1

Structural isomers of n-hexane

Let's think about all of the side-chain configurations that hexane (six carbons) can have, omitting the hydrogens. First there's n-hexane, the simplest:

Next we'll remove one methyl (CH₃) group from the end and put it in a branched position. Notice that if we'd put this "branch" on positions 1 or 5 below, we'd just have n-hexane back, so those don't count. If the methyl group is on the second carbon, the new compound is 2-methyl pentane.

If we move that methyl group to the middle carbon, we get 3-methyl pentane. Notice that if we moved it to the 4^th position, we could turn it around and just get 2-methyl pentane back, so that's redundant.

Now we can take another methyl group from the end of the main (pentane) chain and make a twice-branched alkane, 2,3 dimethyl pentane.

Example 2

Structural isomers of n-heptane

There are nine structural isomers of heptane, C₇H₁₆. We begin with the simplest, normal heptane,

Next we can pull of the end methy group and form two methyl isomers, 2 methyl hexane and 3 methyl hexane. Notice that 4- and 5- methyl hexanes would be redundant.

Next, we can lop off another methyl group and form four unique dimethyl pentanes,

On to double bonds: alkenes

OK, now what if a hydrocarbon contains a double bond. Let's look at the simplest, ethene, more commonly called ethylene, because that name stuck before the official naming rules were widely adopted.

Note that there is no methene, because meth-anything only has one carbon, so there can't be a C=C bond.

For larger unbranched hydrocarbons containing just one double bond, we simply add a number that gives the location of the double bond along the chain. The next-larger alkene is propene. We could name it 1-propene, but that would be redundant because 2-propene is just 1-propene flipped end-to-end.

The next alkene with only one double C=C bond is 1-butene.

Alkenes with more than one double bond

As long as each carbon has four (and only four) bonds, we can form alkenes with two double bonds. These are referred to as dienes. The simplest example is propadiene, here:

If we add another carbon to the main chain, there are two structural isomers of butadiene, this one, 1,2 butadiene:

and this one, 1,3 butadiene:

Compounds like these last two can also be written on one line, like this: cys CH₂CHCHCH₂ and trans CH₂CHCHCH₂

Now while we're here, let's talk about some other kinds of substitution. First we'll put a methyl group on a butadiene molecule:

Notice that the 1 and 3 number the double bond locations and the 2 numbers the second carbon from the end, neither end being unique in this case. This compound could also be written with a one-line formula like this: CH₂C(CH₃)CHCH₂. Notice that the "branch" methyl group is written in parentheses to show that it's not part of the main (longest) chain.

Now here's a 1,3 butadiene with a chlorine atome (chloro) and a bromine atom (bromo) attached at the second and fourth carbons, respectively:

Triple bonds: alkynes

Carbon atoms can also triple-bond to other carbon atoms. Organic molecules that contain one or more triple bonds are called alkynes. The simplest alkyne is ethyne, commonly called acetylene. It may be familiar to you as a gas commonly used in welding.

Like alkenes, the triple bond is rigid — it doesn't rotate about the bond axis. Triple bonds are also the strongest of the C—C bonds. We can make other alkynes. Here are some simple ones:

Notice that we can call this 1,3 butadiyne (di for two triple bonds or "ynes"), but it's really redundant. The bonding restrictions of carbon atoms don't allow for adjacent triple bonds. Butadiyne is pronounced Buta·di'·ine, with all long i's.

Here's another example, 2 pentyne,

Cyclic organic compounds

As you may remember from your work with Lewis structures or with molecular models, carbon compounds can be cyclic, with the —C-C-C— backbone forming a ring. Look, for example, at cyclopentane, below.

Cyclopentane is named as all normal alkanes that form rings, by appending the prefix cyclo to the main chain name. Here is cyclobutane — four carbons arranged in a ring and saturated with as many hydrogens as the carbons can accept:

Ring strain

Now we should note that cyclobutane is not as stable a molecule as cyclopentane. That's because there is a considerable amount of orbital overlap between the molecular orbitals in forming such a small ring. We call that kind of overlap steric hindrance. Chemically speaking, it is easier to break or open the cyclobutane ring than the cyclopentane ring. The cyclohexane ring (see below) is the most stable of the smaller ring compounds because the tetrahedral angles of the C-C bonds are perfectly matched to it.

A. A "paper chemistry" 2-D diagram of cyclohexane showing all of the atoms and bonds. B. As a shorthand, we often represent hydrogen atoms as sticks. It saves time, and it's unambiguous because H atoms can only 'decorate' the outsides of the carbon frameworks. C. A step further: we omit the hydrogens. The reader can assume that if no other atoms are written, the molecule is otherwise 'saturated' with as many hydrogens as it can accommodate. D. A wire-frame model. In this most-common way of representing an organic molecule, carbon atoms lie at any vertex or at the termination of any line segment, and the molecule is assumed to be saturated with hydrogens. E. These 3-D wire-frame representations are important for illustrating 3-D properties of molecules. Cyclohexane can assume a boat-shaped or a chair-shaped (think chaise lounge) configuration. The two hydrogen atoms are there so that the viewer can infer the 3-D arrangement of the others. F. Finally, a space filling model is inconvenient to write when doing paper chemistry, but it's enlightening to get an idea of how the molecule would actually look if we could look directly at the filled molecular orbitals. This model is of the chair configuration of cyclohexane."

cyclic alkenes & aromatic compounds

The most important cyclic alkene is benzene, C₆H₆, shown below. The double bonds of benzene form a resonance structure in which the electrons of the double bonds are delocalized around the ring. Bonding arrangements like this, consisting of alternating single and double bonds in resonance, are called conjugated π systems. Recall from the section or orbital hybridization, that a double bond is often referred to as a π bond.

The wire-frame representation of benzene at the bottom of the figure above is the most common way to represent this molecule "on paper." It nicely captures the idea that the outer electrons of the molecule are more-or-less shared by all of the carbon atoms.