Carbon —The core of organic chemistry
Organic Chemistry—Chemistry of carbon compounds, traditionally excluding "pure" carbon forms, CO, CO2, and CO32–

Electron configuration of carbon atom: 1s2 2s22p2, i.e., 4 VE

Electron/Lewis dot structure: ???

A carbon atom can form single, double, or triple bonds.

Carbon atoms can form covalent bonds with hydrogen atoms,
    e.g., methane (CH4) and propane (C3H8) etc.
    e.g., Carbon-hydrogen bond: C + 4•H ® CH4

with other carbons to build long chains,
    e.g., ethane (H3C—CH3), ethylene (H2C=CH2), etc.

Writing and drawing formulas and structures, e.g., butane, C4H10
1) CH3–CH2–CH2–CH3;     2) CH3CH2CH2CH3;     3) CH3(CH2)2CH3
4) C—C—C—C;     5) Draw all atoms.

with other elements,
    such as O (e.g., ethanol, H3C—CH2—OH)
    N (e.g., amines R–NH2)
    S (e.g., cysteine)
    halogens (e.g., chloroform CHCl3 and Freons, CFCs)

Hydrocarbons—Compounds contains only H and C.

Long chains or rings can be built by C–C linkages to give compounds

Naming hydrocarbons (P. 293)
    1C methane     methyl: —CH3
    2C ethane        ethyl: —CH2CH3
    3C propane
    4C butane
    5C pentane
    6C hexane
    7C heptane
    8C octane
    9C nonane
    10C decane

Structural isomers—Compounds with the same formula but different molecular structures
Example: C5H12

Primary (1º, bound to another C), second (2º, 2 other C’s), tertiary (3º, 3 other C’s), and quaternary (4º, 4 other C’s) carbons, see above example.

Multiple bonds
Alkenes contain C=C double bonds
    e.g., ethene (ethylene) C2H4, propene (propylene) C3H6

Geometric isomers—due to the rigidity without free rotation along the C=C bond (whereas single bond can have free rotation)
    Examples: cis and trans 2-butene/pentene, etc.

Alkynes—containing triple bonds

Reactions on >C=C<
    Hydrogenation: adding H atoms to "saturate" the double bond for the preparation of margarine.
        >C=C< + H2 (+catalyst) ® >CH–CH<

    Hydration with water: formation of alcohol
        >C=C< + H2O (+catalyst) ® >CH–COH<

    Halogenation with HX or X2
        >C=C< + HCl (+catalyst) ® >CH–CCl<
        >C=C< + Br2 (+catalyst) ® >CBr–CBr<

        n H2C=CH2 (+catalyst) ® –(CH–CH)n– (polyethylene, PE)

Aromatic compounds: a fundamental structural motif of drugs
    e.g., benzene (C6H6)


Sources of hydrocarbons: Petroleum, natural gas, and coal

Petroleum refining—Partial distillation of crude oil into fractions of HCs according to boiling point

Cracking—a controlled process by which catalysts are used to break down or rearrange natural HCs into more useful molecules, such as high-octane gasoline.

Properties of HCs and their substituents:
    hydrophobicity—essential property in proteins
    to be functionalized—producing other useful compounds
    completely oxidized to produce H2O and CO2—the greenhouse gas

Alcohols and phenols— Compounds containing R–OH group
    H–O–H (replacement of one H by R) ® R–OH (alcohol)
    R–OH (replacement of H by R’) ® R–O–R’ (ether)

The –OH group can be involved in H-bonding.

    alkane ® alkanol
    methane ® methanol
    ethane ® ethanol


Dehydration to form alkenes (the reverse reaction of alkene hydration), or ether
    CH3CH2CH2–OH (H2SO4, 180º) ® CH3CH=CH2
    2 R–OH (H2SO4, 140º) ® R–O–R + H2O

Oxidation to form aldehydes (1º alcohol, with the –OH attached to a 1º carbon) or ketones (2º alcohol). 3º alcohols are not oxidized into other compounds under mild conditions.

Esterification: forming esters with carboxylic acids

solvent, anesthetics, etc.

Formed via dehydration of alcohols

Thiols: Distinct odors!!
    e.g., from skunk, natural gas additive (ethanethiol which we can sense at 0.1 ppb).

Aldehydes and Ketones in nature: flavors of almond, cinnamon, vanilla, mint, and butter; hormones; sugars; etc. cf. PP. 406, 407.
    Both contain a >C=O group

Change the ending -e of the alkanes into -al for aldehydes and into -one for ketones, e.g., propane ® propanal or propanone (P. 410)


Oxidation of aldehydes gives carboxylic acids, whereas ketones are not oxidized under mild conditions.
    RCHO (oxidation) ® RCOOH

Reductions of aldehydes and ketones give 1º and 2º alcohols, respectively.
    In human body, the carbonyl group >C=O can be reduced by nicotinamide adenine dinucleotide (NADH) in association with enzymes, e.g., reduction of pyruvic acid. See P. 421.

"Derivatives" of ammonia with –R group(s): 1 R, 1º amines; 2 R’s, 2º amines; and 3 R’s, 3º amines. All amino acids have 1º amino group except proline, which has a 2º amino group (P. 589).

Naming: "Alkyl" + amine, e.g., methylamine, butylamine, etc.

Amines can be in cyclic structures, as found in the amino acid histidine, in nucleic acids, in vitamine B, opium alkaloids, nicotine, caffeine, cocaine, etc.

Physical properties:  

Controlled by the bond polarity and H-bonding

Carboxylic acids— Contain a –COOH group
Can be formed by oxidation of 1º alcohols or aldehydes.

Naming: Change the ending -e in alkanes to –oic acid.
    e.g., butane ® butanoic acid

Physical properties of carboxylic acids are controlled by their bond polarity and H-bonding, cf. PP. 438 and 439.

Carboxylic acids in nature: formic acid, acetic acid, citric acid, lactic acid, pyruvic acid, amino acids, etc.

Soaps are sodium of potassium salts of long-chain carboxylic acids (or fatty acids). The long chains are hydrophobic that interact with grease-like stuff, and the –COONa+ (or K+) part is hydrophilic that interact with water and makes soap "soluble" in water (which actually forms micelles). What would happen to soap if the water is "hard"? (See P. 445)

1) Form esters with alcohols, e.g., formation of aspirin, formation of heroin from morphine via simple acetylation, etc.
    R–COOH + R’OH ® R–CO–OH + H2O
    Thus, the reverse reaction is the hydrolysis of esters.

    Reaction of a dicarboxylic acid with a diol can produce a polymer, a polyester.
        HOOC–R–COOH + HO–R’–OH ® HOOC–R–COO–R’–OH + H2O
        Add another acid ® another diol …® ® ® ® a polyester!!

2) Form amides with amines, e.g., formation of peptide bonds (linking amino group of one amino acid with the carboxyl group of another amino acid)
    R–COOH + R’NH2 ® R–CO–NHR + H2O
    Thus, the reverse reaction is the hydrolysis of amide bonds, including the hydrolysis of a peptide bond.

Reaction of a dicarboxylic acid with a diamine can produce a polymer, e.g., nylone-66 is formed by linking 1,6-hexandioic acid with 1,6-hexanediamine:
    HOOC(CH2)4COOH + H2N(CH2)6NH2 ® –(CO(CH2)4–CONH–(CH2)6NH)n

How about formation of proteins? See P. 595.

Both the >C=O group and the NH group can be involved in H-bonding.

Phosphoric acid can also form esters, phosphoesters, which are the backbone of nucleic acids!!