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Chapter 20

Organic and Chemistry

Shaun Williams, PhD

Organic Chemistry and Biochemistry

Hydrocarbons

Isomerism in Alkanes

Butane

The two isomers of butane. One isomer has four carbon atoms in a linear arrangement with single bonds between them. The other isomer has one carbon atom in the center attached to three carbons atoms around it with single bonds.

Rules for Naming Alkanes

  1. For alkanes beyond butane, add –ane to the Greek root for the number of carbons.
  2. $$ \chem{CH_3–CH_2–CH_2–CH_2–CH_2–CH_3} = \text{hexane} $$

  3. Alkyl substituents: drop the –ane and add –yl.
  4. $$ \chem{C_2H_6}\text{ is ethane} $$

    $$ \chem{C_2H_5}\text{ is ethyl} $$

  5. Positions of substituent groups are specified by numbering the longest chain sequentially. The numbering is such that substituents are at lowest possible number along chain.
  6. $$ \begin{align} &\chem{CH_3} \\ &\,| \\ \chem{CH_3-CH_2-} &\chem{CH-CH_2-CH_2-CH_3} \end{align} $$

    3-methylhexane

Rules for Naming Alkanes Continued

  1. Location and name are followed by root alkane name. Substituents in alphabetical order and use di–, tri–, etc.
  2. $$ \begin{align} &\chem{\underset{|}{C}H_3\phantom{-}\underset{|}{C}H_3}\\ \chem{CH_3-CH_2-} &\chem{CH-CH-CH_2-CH_3} \\ \end{align} $$

    3,4-dimethylhexane

Selected Properties of the First Ten Normal Alkanes

Name Formula Molar Mass Melting Point
(\({}^\circ\mathrm{C}\))
Boiling Point
(\({}^\circ\mathrm{C}\))
Number of Structural Isomers
Methane \(\chem{CH_4}\) 16 -182 -162 1
Ethane \(\chem{C_2H_6}\) 30 -183 -89 1
Propane \(\chem{C_3H_8}\) 44 -187 -42 1
Butane \(\chem{C_4H_{10}}\) 58 -138 0 2
Pentane \(\chem{C_5H_{12}}\) 72 -130 36 3
Hexane \(\chem{C_6H_{14}}\) 86 -95 68 5
Heptane \(\chem{C_7H_{16}}\) 100 -91 98 9
Octane \(\chem{C_8H_{18}}\) 114 -57 126 18
Nonane \(\chem{C_9H_{20}}\) 128 -54 151 35
Decane \(\chem{C_{10}H_{22}}\) 142 -30 174 75

The Most Common Alkyl Substituents and Their Names

Structure Name Structure Name
\(\chem{-CH_3}\) Methyl \(\begin{align} &\chem{CH_3} \\ &\,| \\ \chem{-} &\chem{C-CH_3} \\ &\,| \\ &\chem{CH_3} \end{align}\) tert-Butyl
\(\chem{-CH_2CH_3}\) Ethyl
\(\chem{-CH_2CH_2CH_3}\) Propyl
\(\chem{CH_3\overset{|}{C}HCH_3}\) Isopropyl
\(\chem{-CH_2CH_2CH_2CH_3}\) Butyl
\(\chem{CH_3\overset{|}{C}HCH_2CH_3}\) sec-Butyl
\(\begin{align} &\chem{H} \\ &\,| \\ \chem{-CH_2-} &\chem{C-CH_3} \\ &\,| \\ &\chem{CH_3} \end{align}\) Isobutyl

Exercise

Name each of the following:

  1. A six carbon chain. Two CH3 groups on the second carbon. A CH3 group in the fourth carbon. A CH3 group in the fifth carbon.
  2. 2,2,4,5-tetramethylhexane

  3. A seven carbon chain. Two CH2CH3 groups on the second carbon. A CH2CH3 group on the fifth carbon.
  4. 3,6-diethyl-3-methyloctane

Combustion Reactions of Alkanes

Substitution Reactions of Alkanes

Dehydrogenation Reactions of Alkanes

Cyclic Alkanes

The Chair and Boat Forms of Cyclohexane

The chair form of cyclohexane has carbon atoms of the left and right (across from each other in the ring) one up and one down. The boat form has them both up.

Hydrocarbons

Rules for Naming Alkenes

  1. Root hydrocarbon name ends in –ene.
  2. $$ \chem{C_2H_4}\text{ is ethene} $$
  3. With more than 3 carbons, double bond is indicated by the lowest–numbered carbon atom in the bond.
  4. $$ \chem{CH_2=CH–CH_2–CH_3}\text{ is 1-butene} $$

Rules for Naming Alkynes

Exercise

Name each of the following:

  1. A six carbon chain. Methyl groups on carbon atoms 2, 4, and 5. There is a double bond between atoms 4 and 5.
  2. 2,3,5-trimethyl-2-hexene

  3. A seven carbon chain. Ethyle groups on carbon atoms 2 and 5. There is a double bond between atoms 2 and 3.
  4. 6-ethyl-3-methyl-3-octene

More Reactions

Aromatic Hydrocarbons

Benzene (Aromatic Hydrocarbon)

The angle between any three side-by-side carbon atoms in a benzene ring is \(120^\circ\). There are alternating single the double bonds around the six membered ring. There are two resonance forms of benzene. Often we symbolize it by a hexagon with a circle in the middle.

Aromatic Hydrocarbons Continued

More Complexe Aromatic Systems

Name Use or Effect
Naphthalene Formerly used in mothballs
Anthracene Dyes
Phenanthrene Dyes, explosives, and synthesis of drugs
3,4-Benzpyrene Active carcinogen found in smoke and smog

Hydrocarbon Derivatives

The Common Functional Groups

Class Functional Group General Formula Example
Halohydrocarbons \(\chem{-X}\text{ (F, Cl, Br, I)}\) \(\chem{R-X}\) \(\chem{CH_3I}\) iodomethane (methyl iodide)
Alcohols \(\chem{-OHX}\) \(\chem{R-OH}\) \(\chem{CH_3OH}\) methanol (methyl alcohol)
Ethers \(\chem{-O-}\) \(\chem{R-O-R'}\) \(\chem{CH_3OCH_3}\) dimethyl ether
Aldehydes \(\begin{align} &\underset{||}{\chem{O}} \\ \chem{-}&\chem{C-H} \end{align}\) \(\begin{align} &\underset{||}{\chem{O}} \\ \chem{R-}&\chem{C-H} \end{align}\) \(\chem{CH_2O}\) methanal (formaldehyde)
Ketones \(\begin{align} &\underset{||}{\chem{O}} \\ \chem{-}&\chem{C-} \end{align}\) \(\begin{align} &\underset{||}{\chem{O}} \\ \chem{R-}&\chem{C-R'} \end{align}\) \(\chem{CH_3COCH_3}\) propanone (dimethyl ketone or acetone)
Carboxylic acids \(\begin{align} &\underset{||}{\chem{O}} \\ \chem{-}&\chem{C-OH} \end{align}\) \(\begin{align} &\underset{||}{\chem{O}} \\ \chem{R-}&\chem{C-OH} \end{align}\) \(\chem{CH_3COOH}\) ethanoic acid (acetic acid)
Esters \(\begin{align} &\underset{||}{\chem{O}} \\ \chem{-}&\chem{C-O-} \end{align}\) \(\begin{align} &\underset{||}{\chem{O}} \\ \chem{R-}&\chem{C-O-R'} \end{align}\) \(\chem{CH_3COOCH_2CH_3}\) ethyl acetate
Amines \(\chem{-NH_2}\) \(\chem{R-NH_2}\) \(\chem{CH_3NH_2}\) aminomethane (methylamine)

Polymers

Common Synthetic Polymers and Their Monomers and Applications

Monomer Polymer
Name Formula Name Formula Uses
Ethylene Two carbon atoms double bonded to each other. Polyethylene Repeating units of CH2 groups. Plastic piping, bottles, electrical insulation, toys
Propylene CH2 double bonded to a carbon atom with a CH3 group and a hydrogen atom singly bonded to it. Polypropylene Repeating units of CH singly bonded to a CH2 group. The first C has a side CH3 group singly bonded to it. Film for packaging, carpets, lab wares, toys
Vinyl chloride CH2 double bonded to a carbon atom with a Cl atom and a hydrogen atom singly bonded to it. Polyvinyl chloride (PVC) Repeating units of CH2 singly bonded to a CH group. The second C has a side Cl group singly bonded to it. Piping, siding, floor tile, clothing, toys

More Common Synthetic Polymers and Their Monomers and Applications

Monomer Polymer
Name Formula Name Formula Uses
Acrylonitrile CH2 double bonded to a carbon atom with a CN group and a hydrogen atom singly bonded to it. Polyacrylonitrile (PAN) Repeating units of CH2 singly bonded to a CH group. The second C has a side CN group singly bonded to it. Carpets, fabrics
Tetrafluoroethylene Two carbon atoms double bonded to each other. Each carbon has two fluorine atoms attached. Teflon Repeating units of CH2 groups. Each carbon atom has two fluorine atoms attached. Cooking utensils, electrical insulation, bearings

Even More Common Synthetic Polymers and Their Monomers and Applications

Monomer Polymer
Name Formula Name Formula Uses
Styrene CH2 double bonded to a carbon atom with a benzene ring group and a hydrogen atom singly bonded to it. Polystyrene Repeating units of CH2 singly bonded to a CH group. The second C has a side benzene ring singly bonded to it. Containers, thermal insulation, toys
Butadiene CH2 doubly bonded to a CH group singly bonded to a CH group doubly bonded to a CH2 group. Polybutadiene Repeating units of CH2 singly bonded to a CH group doubly bonded to a CH group singly bonded to a CH2 group. Tire tread, coating resin
Butadiene and styrene See previous entries. Styrene-butadiene rubber Repeating units of a six carbon atom chain with a double bond between the carbon atoms 4 and 5. Also, a benzene ring is bonded the the first carbon atom. Synthetic rubber

Types of Polymerication

Proteins

\(\alpha\)-Amino Acids

Bonding in \(\alpha\)-Amino Acids

Levels of Structure in Proteins

Hydrogen Bonding in \(\alpha\)-Helical Arrangement of a Protein Chain

Hydrogen bonding among the side groups in a long amino acid chain hydrogen bond to each other in such a way as to allow the chain to wrap itself around an imaginary axis into a helical arrangement.

Pleated Sheet

Hydrogen bonding among the side groups in a long amino acid chain hydrogen bond to each other in such a way as to allow the chain to flatten itself around onto an imaginary plane.

Carbohydrates

Some Important Monosaccharides

Carbohydrates

The Disaccharide Sucrose is Formed From α-D-glucose and Fructose

An OH group on alpha-D-glucose reacts with the OH group on fructose to form sucrose.

Nucleic Acids

Nucleotides

Deoxyribose (in DNA) and Ribose (in RNA)

Both species are identical five membered rings. Ribose has one more OH group attached to the ring than deoxyribose.

The Organic Bases Found in DNA and RNA

The five organic bases in DNA and RNA. Uracil (U, in RNA), cytosine (C, in both), thymine (T, in DNA), adenine (A, in both), and guanin (G, in both).

DNA

Hydrogen Bonding in DNA

In DNA, thymine can hydrogen bond with adenine while cytosine can hydrogen bond with guanine. It's these hydrogen bonds that cause the DNA to wrap into a double helix as well as holding the two chains together.

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