CHAPTER 5THE WONDERFUL WORLD OF CARBON: ORGANIC

CHEMISTRY AND BIOCHEMICALS

From Green Chemistry and the Ten Commandments of Sustainability, Stanley E. Manahan, ChemChar Research,

Inc., 2006manahans@missouri.edu

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 (C8H18), give the number of each kind of atom in a molecule of a compound.

The formula of C8H18, 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

3-ethyl-2,5-dimethylhexane

n-heptane

Cyclohexane

propeneAcetylene

HC

HH

C H

HCHH

CHH

CH

HCH

H

H

H

C

H

H

C

H

H

C

H

H

C

H

H

C

H

H

C

H

H

CH

H

H

H

H

H

C

HHC

H

C

H

H

H

C

H

C

C

H

C

H

H

C

H

C

H

H

H

CH

H

H

HCCHHC

H

H

HC

H

HC

Names of Hydrocarbons and Other Organic Compounds

Alkanes and alkyl groups

H C H

H

H

C H

H

HH C C

H

H

H

H

H

Methane (CH 4) Methyl group (CH3) Ethane (C2H6) Ethyl group (C2H5)

C C

H

H

H

H

H

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 5.1The 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 (C2H5) 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

C3H8 + 5O2 3CO2 + 4H2O + heat (9.2.1)

• Major source of fossil fuel energy

Substitution reactions

CH4 + 2Cl2 CH2Cl2 + 2HCl (9.2.2)

Alkenes and Alkynes

Two common alkenes and an alkyne

C C

C C

H

HH

HH

H H C C H

Ethylene 1,3-Butadiene

Acetylene

C C

H

HH

H

Double bonds, 4 shared electrons

Triple bond, 6 shared electrons

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:

H C C

H H

H

H H

+ H H

H

C C

H

H H

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.)

(5.2.3)C C C C CH

H

H H

H

H

H H

C

H

H

H

H

C CH

H

H

H+C C

H

H

H

H+C C

H

H

H

H

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, C6H6

H

H

H

H

H

H C

C

C

C

C

C

H

H

H

H

H

H

C

C

C

C

C

C

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.

Naphthalene, C 10 H8

C C H

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

Benzo(a)pyrene, C 20H12

C H

C

Aromatic Compounds

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

x

Toluene Aniline PhenolOHNH2CH3

Fig 5.3. Lines Showing Structural Formulas

C

H

H

Carbons single-bondedto 2 other carbons,

1,3-ButadieneDouble-bonded middle carbon, C

H

Double-bonded end carbon, CH

HC C C CH

H

H

H

H

H

Middle carbons, C

H

H

End carbon, C H

H

Hn-Hexane

Cyclohexane

C

CC

C

CC

H HH

H

HH

H HH

H

HH

C C C C C C HH

H H H H H H

H H H H H H

Fig 5.3. Lines Showing Structural Formulas (Cont.)

CH H

C HH

H

C C C C CH

H

H H H H

H H

H

CH

H

H

2,3-Dichlorobutane

C

H

Cl

Cl

ClC C C CH

H

H H H

H

H

Cl

Cl H

3-Ethyl-3-methylpentaneEthyl group, C2H5

Methyl group, CH3

C HCarbon on aromatic ring,

End carbon, C H

H

H

Toluene

CH

H

H

5.4. Functional Groups

Ethylene oxide Ethanol (alcohol) Acetone (ketone) Butyric acid

OCC

H H

H H

(carboxylic acid)

Methyltertiarybutyl ether, MTBE (an ether)

C

H

HH

H

H

C OH CH

H

C

H

H

O

CH H C OHH

H

C

O

C

H

H

H

H

H

C

HH

H

C

H

H

H

H

C

H

C

COH

H

H

C

H

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

C

O

OH

Formaldehyde Acetaldehyde

H C

H

H

C H

O

CH H

O

Esters are formed by the reaction of an alcohol and an acid

Propyl alcohol Acetic acid

+

+ H2OPropyl acetate ester

OH

H

H

C

H

H

C

H

H

CH H

H

H

CHO C

O

HC

O

H

H

CO

H

H

C

H

H

CH C

H

H

(5.4.1)

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.

MethylamineH C

H

H

NH

H

Nitromethane is used in chemical synthesis and racing car fuel.

NitromethaneH C

H

H

NO2

DimethylnitrosamineH C

H

H

N C H

H

H

N

O

Organohalide Compounds

C ClCl

Cl

Cl

F C F

Cl

Cl

C CH

H

Cl

HC C

Cl

Cl

Cl

H

Cl

Cl

Cl Cl

Cl

Cl

Carbon tetrachloride Dichlorodifluoromethane(Both of these compounds are alkyl halides.)

Vinyl chloride Trichloroethylene(These compounds are alkenyl halides.)

Chlorobenzene A polychlorinated biphenyl (PCB)(These compounds are aromatic halides.)

Organosulfur and Organophosphorus Compounds

Most common examples are thiols, noted for their foul odors

DimethylsulfideMethanethiol C S

H

H

H

C H

H

HC SH

H

H

H

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.

Malathion

C2H5

C2H5

O

O

O

S

P NO2

C2H5

C2H5CH3

H3C

C

O

O

C C

O

H

HO P

S

O

H

S C

O

Parathion

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.

Polymer containing many units oftetrafluoroethylene per molecule,where n is a very large number

Many tetrafluoroethylene monomer molecules

n

.... ....

....++++ CF

FC

F

FF

FC C

F

FF

FC C

F

FC

F

FF

FC

C

F

FF

F

C

F

F

C

F

F

C

F

F

C

F

F

C

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

Propylene(polypropylene) C C

H

H

H

H3Cn

Applications requiringharder plastic, luggage,bottles, outdoor carpet

Vinyl chloride(polyvinyl chloride)

n

C C

H

H

H

Cl

Thin plastic wrap, hose,flooring, PVC pipe

n

n

C

H

CN H

H

C

n

C CH3C H

CC

H

H

H

H

Styrene(polystyrene)

H

H

H

CC Plastic furniture, plasticcups and dishes, blownto produce Styrofoamplastic products

Acrylonitrile(polyacrylonitrile)

Synthetic fabrics (Orlon, Acrilan,Creslan), acrylicpaints

Isoprene(polyisoprene)

Natural rubber

CH

HH3C

H

C

CH

HClC

H

CH

HC

H

H

HC

HC

CN

HC

CH2H2C

H3CC

Monomer Monomer formula Polymer Applications

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, C12H22O11 is a disaccharideStarch is a polysaccharide, a biopolymer of glucose

• Solar energy to chemical energy • Glucose fermentation to ethanol

• Glucose as raw material for chemical synthesis

CC

C C

C O

H

CH2OH

H

O OH

H

H

OH

H

OCC

C C

C O

H

CH2OH

H

C

OH

H

H

OH

H

OC

C C

C O

H

CH2OH

H

OH

H

H

OH

H

O

Three units of the starch macromolecule

HO OH

H

OH

H

H

OH

H

CH2OH

H

OC

CC

C C

Glucose

Generation of glucose by photosynthesis:

6CO2 + 6H2O

C6H12O6 + 6O2

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:

C OHO

C

H

HH2N

Glycine Cysteine TyrosineC OHO

CH

H2N

SH

HH CC OHO

CH

H2N

OH

HH C

CO

CH

N

OH

HH C

HCO

C

H

HN

CH H

SH

NHC

OC

HH

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)

C C C C C C C C C C C C C C C C C C HO H H H H H H H H H H H H H H H H H

H H H H H H H H H H H H H H H H HOC

C OHHHHHHHHHHHHHHHHH

HHHHHHHHHHHHHHHHHOHCCCCCCCCCCCCCCCCCC

C OHHHHHHHHHHHHHHHHH

HHHHHHHHHHHHHHHHHOHCCCCCCCCCCCCCCCCCC

HH

H

HH

Triglyceride of stearic acid, CH 3 (CH2 )16 C(O)OH

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:5.10. NUCLEIC ACIDS

β-D-Ribo-furanose

2-Deoxy- β-D-ribofuranose

P

O-

OO

CC

C C

CN

C

CC

N

O

O

H CH3

HCH2O

HH H

H

H

O

CN

C

CC

N

O

O

H

H

H

O

H

OH

HHH

CH2

CC

C C

OO

O

O-

P

Thymine(DNA only) Uracil (RNA

only)

These nitrogenous bases occur in both DNA and RNA

Nucleotide of DNA Unit of RNA polymer Dashed lines show bonds to next nucleotide unit.

CN

C

CC

N

NH2

O

H H

H

H Cytosine Adenine Guanine

NC

CC

N

CN

C

N

H

H

NH2

HN

C

CC

N

CN

C

NH

O

H2N

H

H

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