CHAPTER 5 THE WONDERFUL WORLD OF CARBON: ORGANIC CHEMISTRY AND BIOCHEMICALS From Green Chemistry and the Ten Commandments of Sustainability, Stanley E. Manahan, ChemChar Research, Inc., 2006

5.1. RINGS AND CHAINS OF CARBON ATOMS Most carbon-containing compounds are organic chemicals and are addressed by the subject of organic chemistry Carbon atoms can form straight chains, branched chains, and rings as well as single, double, and triple bonds so that there are millions of known carbon (organic) compounds:

Organic Chemicals Organic chemicals include Synthetic polymers Agricultural chemicals Important industrial compounds Biological materials Pollution of the water, air, and soil environments by organic chemicals is an area of significant concern. Chemically, most organic compounds can be divided among Hydrocarbons Oxygen-containing compounds Nitrogen-containing compounds Sulfur-containing compounds Phosphorus-containing compounds Organohalides Combinations of these kinds of compounds All organic compounds contain carbon Most organic compounds contain hydrogen, at least one C-H bond The simplest organic compounds are hydrocarbons composed only of carbon and hydrogen

5.2. COMPOUNDS OF CARBON AND HYDROGEN: HYDROCARBONS Alkanes Alkanes, also called paraffins or aliphatic hydrocarbons, are hydrocarbons in which the C atoms are joined by single covalent bonds (sigma bonds) consisting of two shared electrons Straight-chain alkanes Branched-chain alkanes Cycloalkanes

Hydrocarbons (Cont.) Formulas of alkanes Molecular formulas, such as that of octane (C 8 H 18 ), give the number of each kind of atom in a molecule of a compound. The formula of C 8 H 18, for example, may apply to several alkanes, each one of which has unique chemical, physical, and toxicological properties. These different compounds are designated by structural formulas showing the order in which the atoms in a molecule are arranged. Compounds that have the same molecular, but different structural, formulas are called structural isomers.

Figure 5.1. Some Examples of Hydrocarbons Showing the Bonding Diversity of Carbon

Names of Hydrocarbons and Other Organic Compounds Alkanes and alkyl groups Names of alkanes and organic nomenclature Systematic names, from which the structures of organic molecules can be deduced, have been assigned to all known organic compounds. The more common organic compounds, including many toxic and hazardous organic sustances, likewise have common name.

Naming of Alkanes in Figure 5.1 The fact that n-heptane has no side chains is denoted by “ n ”, that it has 7 carbon atoms is denoted by “ hept, ” and that it is an alkane is indicated by “ ane. ” The names of compounds with branched chains or atoms other than H or C attached make use of numbers that stand for positions on the longest continuous chain of carbon atoms in the molecule. For the second compound in Figure 5.1, the hexane part of the name comes from the fact that it is an alkane with 6 carbon atoms in its longest continuous chain. Because it has an ethyl group (C 2 H 5 ) attached on the third carbon atom is denoted by 3-ethyl. The two methyl groups on carbon atoms 2 and 5 are shown by 2,5- dimethyl. The name of the compound is 3-ethyl-2,5-dimethylhexane. The cyclic compound with 6 carbon atoms is cyclohexane.

Reactions of Alkanes Combustion reactions C 3 H 8 + 5O 2  3CO 2 + 4H 2 O + heat (9.2.1) Major source of fossil fuel energy Substitution reactions CH 4 + 2Cl 2  CH 2 Cl 2 + 2HCl (9.2.2)

Alkenes and Alkynes Two common alkenes and an alkyne The double and triple bonds in alkenes and alkynes have “ extra ” electrons capable of forming additional bonds, and are therefore said to be unsaturated. Alkenes and alkynes both undergo addition reactions in which pairs of atoms are added across unsaturated bonds as shown by the hydrogenation reaction below:

Addition reactions add to the chemical and metabolic versatility of compounds containing unsaturated bonds and contribute to their generally higher toxicities. The reactivity of unsaturated bonds makes unsaturated compounds much more chemically reactive, more hazardous to handle in industrial processes, and more active in atmospheric chemical processes, such as smog formation. Polymerization reactions of alkenes: Alkenes and Alkynes (Cont.)

Aromatic Hydrocarbons Benzene is the simplest of a large class of aromatic or aryl hydrocarbons. Many important aryl compounds have substituent groups containing atoms of elements other than hydrogen and carbon and are called aromatic compounds or aryl compounds. Aromatic compounds have ring structures and are held together in part by particularly stable bonds that contain delocalized clouds of so- called π (pi, pronounced “ pie ” ) electrons. Resonance structures of benzene, C 6 H 6 Benzene and the aromatic benzene ring are represented by a hexagon with a circle

Aromatic Hydrocarbons (Cont.) Many toxic substances, environmental pollutants, and hazardous waste compounds are aromatic compounds. Benzene is a volatile, colorless, highly flammable liquid with many important uses that is hazardous both for its ignitability and toxicity (exposure to benzene causes blood abnormalities that may develop into leukemia). Some aromatic hydrocarbons, such as naphthalene, contain fused rings.

Polycyclic Aromatic Hydrocarbons, Benzo(a)pyrene Formed by the incomplete combustion of other hydrocarbons, a process that consumes hydrogen in preference to carbon. Engine exhausts Wood stove smoke Cigarette smoke Charbroiled food Coal tar Petroleum residues Toxicological concern because of conversion to metabolites that can cause cancer

Aromatic Compounds Compounds that contain at least one element other than carbon and hydrogen x

Fig 5.3. Lines Showing Structural Formulas

Fig 5.3. Lines Showing Structural Formulas (Cont.)

5.4. Functional Groups Organo-oxygen compounds Ethylene oxide is a toxic sweet-smelling, colorless, flammable, explosive gas used as a chemical intermediate, sterilant, and fumigant. Ethanol is an alcohol, in which the -OH group is bonded to an alkane or alkene (attachment of the -OH group to an aromatic hydrocarbon molecule gives a phenolic compound).

Organo-oxygen Compounds (Cont.) Acetone is a ketone, a class of compounds that has the C=O functional group in the middle of a hydrocarbon chain. Butyric acid, which occurs in butter, is an organic carboxylic acid, all of which contain the functional group, Methyltertiarybutyl ether, MTBE, formerly used as a gasoline additive, is an ether in which an O atom connects 2 C atoms. Aldehydes

Esters are formed by the reaction of an alcohol and an acid Organo-oxygen Compounds (Cont.)

Organonitrogen Compounds Methylamine is a colorless, highly flammable, toxic irritant gas with a strong odor. Dimethylnitrosamine is an N-nitroso compound, all of which contain the N-N=O functional group, and many of which are carcinogenic. Nitromethane is used in chemical synthesis and racing car fuel.

Organohalide Compounds

Organosulfur and Organophosphorus Compounds Most common examples are thiols, noted for their foul odors

Organophosphorus Compounds Most notable examples are organophosphates Many organophosphates are acetylcholinesterase enzyme inhibitors that disrupt nerve function. Parathion and malathion are insecticides. Parathion is now banned because of its toxicity whereas malathion is a relatively safe insecticide because mammals can metabolize it to relatively nontoxic products The military poison nerve gases, such as sarin, are organophosphates.

5.5. GIANT MOLECULES FROM SMALL ORGANIC MOLECULES Synthetic polymers are produced when small molecules called monomers bond together to form a much smaller number of very large molecules. Many natural products, such as cellulose, are polymers (biopolymers).

Polymers (Cont.) Many of the hazards from the polymer industry arise from the monomers used as raw materials. Many monomers are reactive and flammable, with a tendency to form explosive vapor mixtures with air. All monomers used to make synthetic polymers have a certain degree of toxicity; vinyl chloride used to make polyvinyl chloride plastic is a known human carcinogen. Polymers made from toxic monomers are not toxic.

Some Typical Polymers Made Synthetically

5.6. LIFE CHEMICALS Biochemistry is the chemistry of life processes. Living organisms produce biochemicals Proteins Carbohydrates Lipids Nucleic acids Many biochemicals are large macromolecules

5.7. CARBOHYDRATES Biomolecules consisting of carbon, hydrogen, and oxygen Glucose is a monosaccharide Table sugar, C 12 H 22 O 11 is a disaccharide Starch is a polysaccharide, a biopolymer of glucose Solar energy to chemical energy Glucose fermentation to ethanol Glucose as raw material for chemical synthesis Generation of glucose by photosynthesis: 6CO 2 + 6H 2 O  C 6 H 12 O 6 + 6O 2 Carbohydrates and green chemistry Capture of solar energy

5.8. PROTEINS Proteins composed of nitrogen, carbon, hydrogen, oxygen, some sulfur Proteins are macromolecules composed of polymers of many amino acids The example below shows polymerization of three amino acids:

Proteins (Cont.) Protein structure Loss of protein structure, such as is caused by some toxic substances, is denaturation Two major categories of proteins Fibrous proteins (hair, muscles) globular proteins (hemoglobin) Functions of proteins include Nutrient proteins (casein in milk) Structural proteins (collagen) Contractile proteins (muscle) Regulatory proteins (insulin)

5.9. LIPIDS: FATS, OILS, AND HORMONES Other kinds of lipids consist of waxes and steroids, such as cholesterol Steroids act as hormones (chemical messengers) Lipids are biomolecules soluble in organic solvents Many lipids, such as animal fats, are triglycerides of fatty acids Lipids and green chemistry Poorly biodegradable substances may bioaccumulate in lipids Lipids can be valuable raw materials and fuels that can be cultivated as renewable resources

The fundamental nucleotide units of nucleic acids: NUCLEIC ACIDS

Nucleic Acids (Cont.) Nucleic acids are biological macromolecules that store and pass on the genetic information that organisms need to reproduce and synthesize proteins.  -helix structure by Watson and Crick Nucleic acids and green chemistry Hazards of chemical substances to DNA, including cancer Genetic engineering and recombinant DNA technology Transgenic organisms to produce crops with unique characteristics, synthesize pharmaceuticals, and make a variety of useful raw materials