The organic chemistry supplement provides an overview of the field of organic chemistry. Many majors require an entire year of the so-called "O-Chem", so don't think that this is a comprehensive treatment of organic.

The focus of the supplement is on two broad topics: hydrocarbons and functional group classes. In addition, there is a description of the meaning of chemical formulas of different types.

Organic chemistry is the chemistry of carbon compounds. The name arises from the association of these compounds with living organisms. In fact, it was thought for a long time that organic compounds could only be obtained from living organisms and that it wasn't possible to synthesize organic compounds (the vital force theory.) This theory was disproved in 1828 when the German chemist Friedrich Wöhler synthesized urea, an organic compound which is a component of urine, from the inorganic salt ammonium cyanate. [Although ammonium cyanate contains carbon, it is not considered to be an organic compound; other examples of this are carbonic acid (H₂CO₃), the carbonate ion (CO₃)^2- , the cyanide ion (CN)^- , and a few others.]

There are countless organic compounds of all sorts. One of the reasons for this vast number is that carbon can form bonds to itself, making very large chains and rings possible. In addition, carbon forms stable bonds to hydrogen, oxygen, nitrogen, sulfur and the halogens, as well as other atoms. In all organic compounds, however, there is one rule which is not violated: carbon always forms four bonds. We will consider the following types of organic compounds:

1. Hydrocarbons

   Hydrocarbons are compounds of only two elements: carbon and hydrogen. There are many subclasses of hydrocarbons, but we'll consider only the following:

   1. Aliphatic Hydrocarbons - these are compounds in which the bonding electrons are localized between two atoms. In other words, the electrons in the bonds of the molecule don't have the freedom to roam around the molecule.
      1. Non-cyclic aliphatic hydrocarbons
         1. Alkanes - these compounds all have the general formula C_nH_2n+2, where n is a number from 1 to infinity (in a practical sense, the upper limit for n is on the order of several hundred thousand.) The simplest alkane is methane, CH₄. The alkane with two carbons is ethane, C₂H₆. All alkanes with two or more carbon atoms contain carbon-carbon single bonds. The geometry around an alkane carbon is tetrahedral; picture it as a camera tripod, with the carbon at the head of the tripod and the four atoms bonded to the carbon at the end of the four "legs." The bond angle around a tetrahedral carbon is 109°28´, or about 109.5°. You should know the names of the first ten alkanes, from methane to decane. Another reason for a huge number of organic compounds is compounds with the same formula can have a different arrangement of atoms, making them different compounds with different chemical and physical properties. Compounds with the same formula but a different arrangement of atoms are known as isomers. Don't confuse this term with isotopes, which are related nuclei. Hydrocarbons which are bonded such that the carbon atoms are arranged in a continuous fashion, with no branching, are known as straight-chain hydrocarbons. Pentane, C₅H₁₂ (notice that this alkane follows the general formula above) is an example of a straight-chain alkane. The "line" formula for this compound is CH₃CH₂CH₂CH₂CH₃. A common abbreviation for this is the formula C-C-C-C-C. Notice that the hydrogens aren't shown, but that the number of hydrogens on each carbon can be deduced by remembering that carbon always forms four bonds. An isomer of pentane is 2-methylbutane, whose formula can be written as CH₃CH(CH₃)CH₂CH₃. Notice that the methyl (CH₃) group in the middle is bonded to the second carbon atom from the left; it "branches" from the continuous chain made by the first, second, fourth, and fifth carbons (from left to right in the formula above). Thus, it is known as a branched-chain hydrocarbon. Alkanes are named by identifying the longest continuous chain of carbon atoms, and using this as the base name (eight continuous carbons would give a base name of octane), then naming the substituents on the chain and identifying their position with the number of the carbon to which they are bonded. Here's an example: the compound whose formula can be written CH₃CH₂C(CH₃)(C₂ H₅)CH₂CH₂CH(CH₃) CH₂CH₃ is 3-ethyl-3,6-dimethyloctane. Notice that it is an isomer of the straight-chain compound with twelve carbons (C₁₂H₂₆, or dodecane.)
         2. Alkenes - this class of hydrocarbons contain a carbon-carbon double bond. Each carbon of the double bond is attached to three other things: another carbon and two other atoms or groups of atoms, resulting in a planar carbon atom with 120° bond angles around the carbons of the double bond. The other carbon atoms in the alkene are like alkane carbons: each carbon bonded to four other atoms or groups (methyl, ethyl, etc.) Since carbon can only form four bonds, the formation of a double bond requires the elimination of two hydrogens (one from each carbon involved in the double bond.) Thus, the general formula for an alkene is C_nH_2n. The simplest alkene is the one with two carbons: ethene, whose formula is C₂H₄. (Recall that the corresponding alkane, ethane, has a formula of C₂H₆). In addition to the isomers which arise from branching, as in the alkanes, alkenes can form another type of isomers known as cis/trans isomers. The cis isomer has similar groups on the same "side" of the double bond, while the groups in the trans isomer are on opposite sides of the double bond.
         3. Alkynes - this class of hydrocarbons contains a carbon-carbon triple bond. Each carbon involved in the triple bond is bonded to only one other atom or group. The bond angle around each carbon is 180°, resulting in a linear geometry. The other carbon atoms in the alkene are like alkane carbons: each carbon bonded to four other atoms or groups (methyl, ethyl, etc.) The general formula for an alkyne is C_nH_2n-2. The simplest alkyne is ethyne, C₂H₂ (common name: acetylene.)
      2. Cyclic aliphatic hydrocarbons - if a chain of carbon atoms eliminated two hydrogens by bonding end-to-end, a cyclic structure is formed. The simplest cyclic hydrocarbon is the three-carbon ring cyclopropane. The three carbons in the ring are at the vertices of a triangle; in fact, a triangle is the common symbol for cyclopropane. Other regular polygons represent larger rings: a square for cyclobutane, a pentagon for cyclopentane, and hexagon for cyclohexane, etc. The hydrogens aren't usually shown, but remember that since each carbon can form four bonds, and there are already two other carbons bonded to a particular carbon, each carbon in a cyclic aliphatic hydrocarbon involving only single bonds is bonded to two hydrogens. Thus, the formula for cyclopropane is C₃H₆; cyclobutane is C₄H₈. Notice that this is the same as the general formula for an alkene, although there are no double bonds. This is because the linking of the two ends of a carbon chain results in the loss of two hydrogen atoms. Cyclic hydrocarbons can also contain double bonds, although each double bond will result in two fewer hydrogens in the molecule. For example, cyclohexane has the formula C₆H₁₂, while cyclohexene has the formula C₆H₁₀.
   2. Aromatic hydrocarbons - these compounds, unlike aliphatic hydrocarbons, have delocalized electrons; i.e., electrons which are free to move throughout the entire molecule. The prototype of this class of compounds is benzene , C₆H₆. This is a cyclic molecule, like cyclohexane, but there are some important differences: 1) there are twice the number of hydrogens in cyclohexane as in benzene; 2) all bonds in cyclohexane are single bonds, while the bonds in benzene are intermediate between single and double bonds. It is common to draw the structure of benzene as a hexagon with alternating single and double bonds, but this is not an accurate picture of the bonding in benzene. In particular, do not think that the double bonds in this structure can "move" around the ring; in fact, as pointed out above, there are no real double bonds in the molecule. The best way to draw benzene is as a hexagon with a circle inside (the circle indicates that some of the electrons in the molecule are delocalized), and the best way to view it is that it is a planar molecule, with all 12 atoms in the plane, and that there are six electrons (three pairs, formally representing three double bonds) which can move freely in a circular area above and below the plane of the molecule.
2. Functional group derivatives of hydrocarbons - these compounds contain certain groupings of atoms (called functional groups because they determine the function, or properties, of the molecule) which can be viewed as replacing a hydrogen atom of an alkane. For example, the functional group which defines an alcohol is the -OH group (the line in front of the oxygen atom indicates that the group is attached to a carbon atom of a hydrocarbon). If we substitute this group for one of the hydrogen atoms in methane, CH₄, we get methyl alcohol, CH₃OH. You will be responsible for recognizing the following classes of functional group derivatives: [Note: the "R" in the general formula represents an alkyl (aliphatic) or aryl (aromatic) group.]
   1. Alcohol: General formula = ROH. If the carbon bonded to the OH group is bonded to only one other carbon, the alcohol is classified as a primary (1°) alcohol. An example of this is grain alcohol, or ethyl alcohol: CH₃CH₂OH. If the carbon bonded to the OH is bonded to two other carbons, the alcohol is secondary (2°). A common example of a secondary alcohol is isopropyl alcohol, also known as isopropanol or 2-hydroxypropane: CH₃CH(OH)CH₃. Note that this compound is an isomer of the primary alcohol n-propanol, CH₃CH₂CH₂OH. As you might expect, tertiary (3°) alcohols are those in which the carbon bonded to the OH is bonded to three other carbons. An example is t-butyl alcohol, where the italicized 't' refers to tertiary. This compound can also be named 2-hydroxy-2-methylpropane: CH₃C(OH)(CH₃)CH₃. Notice that the second carbon from the left is not bonded to any hydrogens.
   2. Ether: General formula = ROR^´ [the prime on the second R group implies that the two R groups do not necessarily have to be the same, although they are allowed to be the same.] Ethers are simply two R groups separately bonded to the same oxygen. In other words, they are structurally like water, except that instead of two hydrogen atoms there are two organic groups. The simplest ether is dimethyl ether, CH₃OCH₃. One of the most common ethers, an extremely flammable solvent, is diethyl ether, C₂H₅OC₂H₅. These two examples represent symmetrical ethers, where the two R groups are the same. An example of an unsymmetrical ether is ethyl methyl ether, CH₃OC₂H₅.
   3. Acid: General formula = RCOOH. Often this group of compounds is called carboxylic acids instead of simply acids. Note that there are three groups bonded to the carbon: R, a doubly-bonded oxygen, and an OH group. The OH, however, has different properties than an alcohol, in that it loses a hydrogen ion relatively easily. This is a result of the electron-withdrawing effect of the carbonyl (C=O) group. The general ionization reaction is represented by
      RCOOH + H₂O -----> RCOO^- + H₃O⁺. The formation of hydronium ion is what makes the substance an acid. The other product of this ionization is called a carboxylate ion. One of the characteristic reactions of an acid is neutralization with a base, which can be represented as
      n RCOOH + M(OH)_n ----> (RCOO)_nM + n H₂O, where M represents some metal, usually a Group IA or IIA metal ion. The simplest carboxylic acid is formic acid, where R = H; the formula is HCOOH. The next acid in the series is the extremely common acid acetic acid (ethanoic acid), the solute in vinegar: CH₃COOH. The carboxylate anion of acetic acid is the acetate ion, CH₃COO^-, often written as C₂H₃O₂^-.
   4. Ester: General formula = RCOOR^´. Don't confuse this class with ethers. An ester is formed by the reaction between a carboxylic acid and an alcohol. In other words, the general reaction is carboxylic acid + alcohol -----> ester + water. This type of reaction is called a condensation reaction: one where two molecules combine to form a larger molecule by splitting off a small molecule (in this case, water.) The two R groups in the general formula may be the same or they may differ. The compound with the formula CH₃COOCH₃ is formed by the reaction between acetic acid (also called ethanoic acid) and methyl alcohol (make sure you understand why these are the reactants), and the name of the ester is methyl acetate (or methyl ethanoate). As an example of an ester where the groups are different, consider the ester formed between benzoic acid (C₆H₅COOH) and ethyl alcohol (C₂H₅OH). The formula of the product is C₆H₅COOC₂H₅, and the name is ethyl benzoate.
   5. Ketone: General formula = RCOR´. Ketones are compounds where a carbonyl group (C=O) is bonded to two organic groups. An example of a symmetrical ketone is dimethyl ketone, CH₃COCH₃. An unsymmetrical ketone would be something like isopropyl phenyl ketone, (CH₃)₂CHCOC₆H₅. Ketones can also be named as a derivative of the parent hydrocarbon, using -one as a suffix and specifying the number of the carbon with the double bond to the carbonyl oxygen. For example, the preferred name for the dimethyl ketone example above is 2-propanone. The common name of this extremely common solvent (used as nail polish remover) is acetone.
   6. Aldehyde: General formula = RCHO. Note that the functional group is written this way to differentiate it from an alcohol, ROH. Keep in mind, however, that the hydrogen is not bonded to the oxygen in an aldehyde - it is bonded to the carbon, which is also doubly-bonded to the carbonyl oxygen. Aldehydes can be considered to be a ketone where one of the R groups is a hydrogen. Because the carbon bonded to the carbonyl oxygen is also bonded to the hydrogen, that leaves only one more bond available to it; this means that the aldehyde functional group will always be at the end of a multicarbon chain, whereas the carbonyl group in a ketone can be anywhere in the middle of a long chain. The simplest aldehyde is formaldehyde (also called methanal), where R = H. The formula is HCHO. Formaldehyde is used as embalming fluid. The aldehyde where R = methyl is acetaldehyde (or ethanal), CH₃CHO.
   7. Amine: General formula = NR₃. [Note: one or two of the R groups may be hydrogen. If all three are H, however, the compound is NH₃ (ammonia), an inorganic compound.] If the nitrogen is bonded to only one R group, i.e., if the formula is RNH₂, the compound is referred to as a primary (1°) amine. An example of this is methylamine, CH₃NH₂. If the nitrogen is bonded to two R groups, i.e., R₂NH, then it is classified as a secondary (2°) amine. Examples of this would be dimethylamine, ethylmethylamine, etc. Finally, if there are three R groups (and, as a consequence, no hydrogens) we have a tertiary (3°) amine. An example of this situation is trimethylamine, (CH₃)₃N. Remember that in all amines, there is a lone pair of electrons on the nitrogen atom.
   8. Amide: General formula = RCONR₂. An amide is the product of a condensation reaction between a primary or secondary amine and a carboxylic acid, e.g. RCOOH + R₂NH -----> RCONR₂ + H₂O. Notice that the hydrogen on the amine combines with the OH on the acid to split off the water molecule. The amide functional group is very important biologically: all proteins are polymers made up of a large number of amide linkages (biochemists call the amide linkages in proteins peptide linkages.)
3. Representation of Formulas
   The "line formula" for ethylenediaminetetraacetic acid (EDTA) is
   (HOOCCH₂)₂NCH₂CH₂N(CH₂COOH)₂,
   but this formula does not give useful visual information about the actual 3-dimensional geometry of the molecule. Three-dimensional structures can be represented in many ways. To see four visual models for the structure of EDTA, click here.

Last modified July 30, 1997