Carbon compounds

    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.

    We must begin our exploration of organic chemistry with a tour of what kinds of organic chemicals exist, their names and how to name them, and the interesting features of each.

    We'll begin with hydrocarbons, compounds made of only carbon and hydrogen, and we'll keep in mind that the orbital hybridization of carbon means that it always forms four bonds, though these may be part of multiple-bonds like double and triple bonds.

    Organic chemistry is the chemistry of carbon-containing compounds.

    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.

    Here's a table of those prefixes and the formulas of the simplest long-chain alkane with that many carbons. You'll need to memorize the prefixes; they're very important in learning organic chemistry.

    Organic chemistry prefixes

    N carbons Prefix Alkane
    1 meth methane   (CH4)
    2 eth ethane   (C2H6)
    3 prop propane   (C3H8)
    4 but butane   (C4H10)
    5 pent pentane   (C5H12)
    6 hex hexane   (C6H14)
    7 hep heptane   (C7H16)
    8 oct octane (C8H18)
    9 non nonane   (C9H20)
    10 dec decane   (C10H22)
    11 undec undecane   (C11H24)
    12 dodec dodecane   (C12H26)

    There are prefixes for larger hydrocarbon chains, but those are more rare, and you can look them up as needed. The first 12 will be just fine for now.

    Here are the structures of some more n-alkanes, just to round things out:

    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.

    Now this particular alkane is a singly-branched alkane. To name it, we begin by numbering the carbons in the longest chain. In this case, there are three. Notice that you can count three carbons in a row in a number of ways:

    These are all the same because we could straighten out the "bent" 1-2-3 chains to recover the one on the left. You'll need to be careful of this kind of thing when counting larger alkane main chains, too.

    We begin the counting at the end of the chain that's most unique. That's a little vague, and there are definitely stricter rules ahead, but it does the trick most of the time. Now in this case, the methyl group, CH3, is in the middle, so it's always on the second carbon of the main chain, no matter which way we number. So this compound is 2-methyl propane, for propane with a methyl group on the second carbon. Notice that we name the side chain accoring to how many carbon atoms it contains; in this case it's one, so that's a meth-yl "group."

    Structural isomers have different properties

    Even though they share the same chemical formula, C4H10, n-butane and 2-methyl propane have different chemical properties. Here are a few for comparison:

    property n-butane 2-methyl propane
    Boiling temp -0.4˚C -11.75˚C
    Energy content 47.39 MJ/Kg 45.59 MJ/Kg
    Vapor pressure
    @ 21˚C
    215 KPa 311 KPa

    Alkanes are hydrophobic

    Alkanes are not polar molecules. There is little possibility for an alkane to have one "end" that is more or less positive or negative than another. For this reason, alkanes are not soluble (don't dissolve) in polar solvents like water. The word hydrophobic means "water fearing." Nonpolar substances are soluble in alkane liquids like hexane. For that reason, hexane is a good solvent for removing greases and waxes, which tend to be made of long-chain alkanes.

    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 4th 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.

    Finally, we can put both of those branches on the same carbon to get 2,2 dimethyl pentane. Notice that we actually write "2, 2" to indicate that there are two branches on the second carbon of the main (butane) chain

    Those are the only five structural isomers of n-hexane.


    It might be tempting to think of placing an ethyl (C2H5—) group on propane, like in the figure below, but if you roll over/tap the figure, you'll see that we could simply renumber it to come up with 3-methyl pentane, which we already listed above. With a little practice, you'll develop an eye for these redundancies.

    2-ethyl butane is also (and more aptly named) 3-methyl 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,

    Taking off another CH3 gives us one trimethyl butane, 2,2,3 trimethyl butane. Notice that our prefix numbering system just continues, covering all of the branches, in this case all methyl groups.

    Finally, we can take an ethyl group (C2H5-) from n-heptane, substitute it at the 3 position and form 3 ethyl pentane.

    Any other structure you might think of is redundant with one of these if you just rearrange it. There are only nine structural isomers of heptane. Like the hexanes, all of these have slightly different properties, but the same molecular formula, C7H16.

    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.

    Now things get a little more interesting. Take a look at 2-butene. Because the C=C pi bond does not rotate around its axis, we can have two structural isomers of 2-butene. The first is cis 2-butene,

    In which both of the methyl groups attached to the double-bonded carbons are on the same side of the double bond (they are said to be cys.), and one in which they are on opposite sides.

    This compound is trans 2 butene, and the methyl groups are said to be in a trans configuration.

    cis & trans alkenes

    Functional groups located across a C=C double bond may be on the same side of the double bond (cys) or on opposite sides (trans). The names of these compounds have the prefix cys or trans (usually in italic), as appropriate.

    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:

    This compound would be more-appropriately named 1-chloro 3-bromo 1,3 butadiene because we tend to make the number locations of our "functional groups," like F, Br, Cl, CH3, OH-, and so on, as small as possible.

    We've used them a few times, so now is a good time for a refresher on the numerical prefixes commonly used in chemistry. For example, the molecule 1,2,3 trichloro propane (CH2ClCHClCH2Cl) has three chlorine atoms, thust the tri in trichloro. Make sure you're familiar with these prefixes at least through 6 (hexa).

    Numerical prefixes

    number prefix
    1 mono
    2 di
    3 tri
    4 tetra
    5 penta
    6 hexa
    7 hepta
    8 octa
    9 nona
    10 deca
    11 undeca
    12 dodeca

    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,

    And finally a more complicated example with a few functional groups:

    This compound could also be numbered from the other end, as 1,1,6 trihydroxy 3-pentyne. Although you're likely to find both names in literature and catalogs, the latter is preferable because we generally begin the main-chain numbering with the most highly substituted end, and in this case that's the one with two hydroxyls (OH). It's important, when searching for a compound by its name, to remember to be flexible in this way. You might discover what you're looking for under a slightly-different name.

    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.

    Cyclopropane, below, is a very sterically hindered or strained ring. When it exists, it isn't usually for long. Collisions can break the ring and reactions with other cyclopropane or other molecules form more stable structures.

    The red shading in this diagram of cyclopropane indicates that the bonds are strained due to steric hindrance.


    Take a look at the figure below, showing several ways of representing cyclohexane on paper. At this point in drawing structures of organic molecules, we're going to need a simpler method; we'll settle on the wire-frame representation.

    It's very instructive to try to build some of these strained ring molecules with a molecular model kit. If you build with rigid balls and sticks, you won't be able to build cyclobutane or cyclopropane. You can with plastic or spring bonds, but you'll notice that you have to bend them in order to get them to fit. Cyclohexane, on the other hand, forms a ring structure quite naturally.

    Notice, also, that the C—C bonds of cyclohexane allow for some flexibility. This ties directly into the reactivity of this molecule, and to the properties of substituted cyclohexanes, like chloro cyclohexane, C6H11Cl.



    Relating to the spatial arrangement of atoms within a molecule, especially as it affects molecular structure and chemical reactions. Often we speak of steric hindrance, which describes the inability of molecules to adopt certain structures because other parts of the molecule are in the way.

    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.

    A space-filling model of benzene looks like this:

    Image: Wikipedia Commons

    Molecules with conjugated π bonding are called aromatic, and they are referred to as aromatics or arenes. The name originates from the strong and likely familiar odors that most aromatic molecules have.

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