Chapter 20

Organic and Chemistry

Shaun Williams, PhD

Organic Chemistry and Biochemistry

Organic Chemistry

The study of carbon-containing compounds and their properties. The vast majority of organic compounds contain chains or rings of carbon atoms.

Biochemistry

The study of the chemistry of living things.

Hydrocarbons

Compounds composed of carbon and hydrogen.
Saturated: C—C bonds are all single bonds.

$$ \text{alkanes } \chem{[C_nH_{2n+2}]} $$

The ethane molecule has two carbons attached to each other with single bonds. Three hydrogen atoms are attached to each of the carbons with single bonds.

Unsaturated: contains carbon–carbon multiple bonds.

Three carbon atoms. Carbon 1 is singly bonded to carbon 2 which is doubly bonded to carbon 3. Carbon one has 3 hydrogen attached to it, carbon 2 has one hydrogen attached to it. Carbon 3 has 2 hydrogens attached to it.

Three carbon atoms. Carbon 1 is singly bonded to carbon 2 which is triply bonded to carbon 3. Carbon one has 3 hydrogen attached to it, carbon 2 has no hydrogen attached to it. Carbon 3 has 1 hydrogens attached to it.

Isomerism in Alkanes

Structural isomerism – occurs when two molecules have the same atoms but different bonds.

Butane and all succeeding members of the alkanes exhibit structural isomerism.

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

For alkanes beyond butane, add –ane to the Greek root for the number of carbons.

$$ \chem{CH_3–CH_2–CH_2–CH_2–CH_2–CH_3} = \text{hexane} $$

Alkyl substituents: drop the –ane and add –yl.

$$ \chem{C_2H_6}\text{ is ethane} $$

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

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.

$$ \begin{align} &\chem{CH_3} \\ &\,| \\ \chem{CH_3-CH_2-} &\chem{CH-CH_2-CH_2-CH_3} \end{align} $$

3-methylhexane

Rules for Naming Alkanes Continued

Location and name are followed by root alkane name. Substituents in alphabetical order and use di–, tri–, etc.

$$ \begin{align} &\chem{\underset{|}{C}H_3\phantom{-}\underset{|}{C}H_3}\\ \chem{CH_3-CH_2-} &\chem{CH-CH-CH_2-CH_3} \\ \end{align} $$

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:

2,2,4,5-tetramethylhexane

3,6-diethyl-3-methyloctane

Combustion Reactions of Alkanes

At a high temperature, alkanes react vigorously and exothermically with oxygen.
Basis for use as fuels.

$$ \chem{2C_4H_{10}(g) + 13O_2(g) \rightarrow 8CO_2(g) + 10 H_2O(g)} $$

Substitution Reactions of Alkanes

Primarily where halogen atoms replace hydrogen atoms.

Dehydrogenation Reactions of Alkanes

Hydrogen atoms are removed and the product is an unsaturated hydrocarbon.

Cyclic Alkanes

Carbon atoms can form rings containing only C-C single bonds.
General formula: $\chem{C_nH_{2n}}$

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

Alkenes: hydrocarbons that contain at least one carbon–carbon double bond. [$\chem{C_nH_{2n}}$]

$$ \chem{CH_3–CH=CH_2}\;\;\;\;\text{propene} $$

Alkynes: hydrocarbons containing at least one carbon–carbon triple bond. [$\chem{C_nH_n}$]

$$ \chem{CH_3–CH_2–C\equiv C–CH_3}\;\;\;\;\text{2–pentyne} $$

Rules for Naming Alkenes

Root hydrocarbon name ends in –ene.
With more than 3 carbons, double bond is indicated by the lowest–numbered carbon atom in the bond.

Rules for Naming Alkynes

Same as for alkenes except use -yne as suffix

Exercise

Name each of the following:

2,3,5-trimethyl-2-hexene

6-ethyl-3-methyl-3-octene

More Reactions

Addition Reactions

Pi bonds (which are weaker than the C-C bonds), are broken, and new $\sigma$ bonds are formed to the $\sigma$ atoms being added.

Halogenation Reactions

Addition of halogen atoms of alkenes and alkynes.

Aromatic Hydrocarbons

A special class of cyclic unsaturated hydrocarbons.
Simplest of these is benzene ($\chem{C_6H_6}$).
The delocalization of the $\pi$-electrons makes the benzene ring behave differently from a typical unsaturated hydrocarbon.

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

Unsaturated hydrocarbons generally undergo rapid addition reactions, but benzene does not.
Benzene undergoes substitution reactions in which hydrogen atoms are replaced by other atoms.

Benzene reacts with molecular chlorine in the presence of iron(III) chloride catalyst to form a benzene ring with a chlorine attached to one of the carbon atoms (chlorobenene) and hydrochloric acid.

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

Molecules that are fundamentally hydrocarbons but have additional atoms or groups of atoms called functional groups.

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

Large, usually chainlike molecules that are built from small molecules called monomers.

Common Synthetic Polymers and Their Monomers and Applications

Monomer		Polymer
Name	Formula	Name	Formula	Uses
Ethylene		Polyethylene		Plastic piping, bottles, electrical insulation, toys
Propylene		Polypropylene		Film for packaging, carpets, lab wares, toys
Vinyl chloride		Polyvinyl chloride (PVC)		Piping, siding, floor tile, clothing, toys

More Common Synthetic Polymers and Their Monomers and Applications

Monomer		Polymer
Name	Formula	Name	Formula	Uses
Acrylonitrile		Polyacrylonitrile (PAN)		Carpets, fabrics
Tetrafluoroethylene		Teflon		Cooking utensils, electrical insulation, bearings

Even More Common Synthetic Polymers and Their Monomers and Applications

Monomer		Polymer
Name	Formula	Name	Formula	Uses
Styrene		Polystyrene		Containers, thermal insulation, toys
Butadiene		Polybutadiene		Tire tread, coating resin
Butadiene and styrene	See previous entries.	Styrene-butadiene rubber		Synthetic rubber

Types of Polymerication

Addition Polymerization

Monomers "add together" to form the polymer, with no other products. (Teflon)

Condensation Polymerization

A small molecule, such as water, is formed for each extension of the polymer chain. (Nylon)

Proteins

Natural polymers made up of $\alpha$-amino acids with molar masses:
Fibrous Proteins: provide structural integrity and strength to muscle, hair and cartilage.
Globular Proteins:

Roughly spherical shape
Transport and store oxygen and nutrients
Act as catalysts
Fight invasion by foreign objects
Participate in the body’s regulatory system
Transport electrons in metabolism

$\alpha$-Amino Acids

$\chem{–NH_2}$ always attached to the $\alpha$-carbon (the carbon attached to $\chem{–COOH}$)

Bonding in $\alpha$-Amino Acids

An OH group on one amino acid reacts with a H on the amine of another amino acid to form a bond. This bonded region is called a peptide linkage.

There are 20 amino acids commonly found in proteins.

Levels of Structure in Proteins

Primary: Sequence of amino acids in the protein chain.
Secondary: The arrangement of the protein chain in the long molecule (hydrogen bonding determines this).
Tertiary: The overall shape of the protein (determined by hydrogen-bonding, dipole-dipole interactions, ionic bonds, covalent bonds and London forces).

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

Food source for most organisms and structural material for plants.
Empirical formula = $\chem{CH_2O}$
Monosaccharides (simple sugars)

pentoses – ribose, arabinose
hexoses – fructose, glucose

Some Important Monosaccharides

D-Ribose
D-Arabinose
D-Ribulose
D-glucose
D-Monnose
D-Galactose
D-Fructose

Carbohydrates

Disaccharides (formed from 2 monosaccharides joined by a glycoside linkage, a $\chem{C—O—C}$ bond between the rings):

sucrose (glucose + fructose)

Polysaccharides (many monosaccharide units):

starch, cellulose

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

DNA (deoxyribonucleic acid): stores and transmits genetic information, responsible (with RNA) for protein synthesis.

(Molar masses = several billion)

RNA (ribonucleic acid): helps in protein synthesis.

(Molar masses from 20,000 to 40,000 g/mol)

Nucleotides

Monomers of the nucleic acids.
Three distinct parts:

A five–carbon sugar, deoxyribose in DNA and ribose in RNA.
A nitrogen–containing organic base.
A phosphoric acid molecule ($\chem{H_3PO_4}$).

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

Key to DNA’s functioning is its double-helical structure with complementary bases on the two strands.
The bases form hydrogen bonds to each other.

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.

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)

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

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

Chapter 20 Organic and Chemistry

Organic Chemistry and Biochemistry

Hydrocarbons

Isomerism in Alkanes

Butane

Rules for Naming Alkanes

Rules for Naming Alkanes Continued

Selected Properties of the First Ten Normal Alkanes

The Most Common Alkyl Substituents and Their Names

Exercise

Combustion Reactions of Alkanes

Substitution Reactions of Alkanes

Dehydrogenation Reactions of Alkanes

Cyclic Alkanes

The Chair and Boat Forms of Cyclohexane

Hydrocarbons

Rules for Naming Alkenes

Rules for Naming Alkynes

Exercise

More Reactions

Aromatic Hydrocarbons

Benzene (Aromatic Hydrocarbon)

Aromatic Hydrocarbons Continued

More Complexe Aromatic Systems

Hydrocarbon Derivatives

The Common Functional Groups

Polymers

Common Synthetic Polymers and Their Monomers and Applications

More Common Synthetic Polymers and Their Monomers and Applications

Even More Common Synthetic Polymers and Their Monomers and Applications

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

Pleated Sheet

Carbohydrates

Some Important Monosaccharides

Carbohydrates

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

Nucleic Acids

Nucleotides

Deoxyribose (in DNA) and Ribose (in RNA)

The Organic Bases Found in DNA and RNA

DNA

Hydrogen Bonding in DNA

Chapter 20

Organic and Chemistry