Organic and Biological Molecules

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Organic and Biological Molecules

• Chapter 22

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Organic Chemistry and Biochemistry

• The study of carbon-containing
• compounds and their properties.
• The vast majority of organic
• compounds contain chains or rings
• of carbon atoms.
• The study of the chemistry of living
• matter

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Hydrocarbons

• compounds composed of carbon and hydrogen.
• Saturated compounds (alkanes) have the maximum
  number of hydrogen atoms attached to each carbon
  atom

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• Unsaturated compounds have fewer hydrogen atoms
  attached to the carbon chain than alkanes
• Unsaturated They contain carbon-carbon multiple
  bonds (double or triple)

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22.1 Alkanes Saturated hydrocarbons

• Saturated hydrocarbons, CnH2n2
• Saturated because they cant take any more
  hydrogen atoms
• Normal straight chains (unbranched hydrocarbons)
• H3C(CH2)n2CH3
• Waxes, oils, fuel gases as n decreases.

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Alkanes Saturated Hydrocarbons
The C-H Bonds in Methane
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The Lewis structure of ethane.
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Propane
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Butane
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The First 10 Normal Alkanes

• Name Formula M.P. B.P. Structural Isomers
• Methane CH4 -183 -162 1
• Ethane C2H6 -172 -89 1
• Propane C3H8 -187 -42 1
• Butane C4H10 -138 0 2
• Pentane C5H12 -130 36 3
• Hexane C6H14 -95 68 5
• Heptane C7H16 -91 98 9
• Octane C8H18 -57 126 18
• Nonane C9H20 -54 151 35
• Decane C10H22 -30 174 75

C1 - C4 are Gases at Room Temperature
C5 - C16 are Liquids at Room Temperature
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IUPAC Rules for Naming Branched Alkanes

• Find and name the parent chain in the hydrocarbon
  - this forms the root of the hydrocarbon name
• Number the carbon atoms in the parent chain
  starting at the end closest to the branching
• Name alkane branches by dropping the ane from
  the names and adding yl. A one-carbon branch
  is called methyl, a two-carbon branch is
  ethyl, etc
• When there are more than one type of branch
  (ethyl and methyl, for example), they are named
  alphabetically
• Finally, use prefixes to indicate multiple
  branches

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Rules for Naming Alkanes

• 1. For alkanes beyond butane, add -ane to the
  Greek root for the number of carbons.
• C-C-C-C-C-C hexane
• 2. Alkyl substituents drop the -ane and add
  -yl
• -C2H5 is ethyl

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Rules for Naming Alkanes

• 3. Positions of substituent groups are specified
  by numbering the longest chain sequentially.
• C
• ??
• C-C-C-C-C-C
• 3-methylhexane
• Start numbering at the end closest to the
  branching
• 4. Location and name are followed by root alkane
  name. Substituents are given in alphabetical
  order and use di-, tri-, etc.

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Normal vs Branched Alkanes

• Normal alkanes consist of continuous chains of
  carbon atoms
• Alkanes that are NOT continuous chains of carbon
  atoms contain branches
• The longest continuous chain of carbons is called
  the parent chain

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Structural Isomerism

• Structural isomers are molecules with the same
  chemical formulas but different molecular
  structures - different connectivity.
• They arise because of the many ways to create
  branched hydrocarbons.

n-pentane, C5H12
2-methlbutane, C5H12
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Example Show the structural formula
of 2,2-dimethylpentane

• The parent chain is indicated by the ROOT of the
  name - pentane. This means there are 5 carbons
  in the parent chain.

• dimethyl tells us that there are TWO methyl
  branches on the parent chain. A methyl branch is
  made of a single carbon atom.
• 2,2- tell us that BOTH methyl branches are on
  the second carbon atom in the parent chain.

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Example Structural formula of
3-ethyl-2,4-dimethylheptane?

• The parent chain is indicated by the ROOT of the
  name - heptane. This means there are 7 carbons
  in the parent chain.

• 2,4-dimethyl tells us there are TWO methyl
  branches on the parent chain, at carbons 2 and
  4.
• 3-ethyl- tell us there is an ethyl branch
  (2-carbon branch) on carbon 3 of the parent
  chain.

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Example 2,3,3-trimethyl-4-propyloctane

• The parent chain is indicated by the ROOT of the
  name - octane. This means there are 8 carbons
  in the parent chain.

• 2,3,3-trimethyl tells us there are THREE methyl
  branches - one on carbon 2 and two on carbon 3.
• 4-propyl- tell us there is a propyl branch
  (3-carbon branch) on carbon 4 of the parent
  chain.

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Example Name the molecules shown

• parent chain has 5 carbons - pentane
• two methyl branches - start counting from the
  right - 2 and 3
• 2,3-dimethylpentane

• parent chain has 8 carbons - octane
• two methyl branches - start counting from the
  left - 3 and 4
• one ethyl branch - 5
• name branches alphabetically

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Reactions of alkanes

• Combustion reactions
• 2C4H10 13 O2 8CO2 10 H2O(g)
• Substitution Reactions

CH4 Cl2 CH3Cl HCl
CH3Cl Cl2 CH2Cl2 HCl
CH2Cl2 Cl2 CH Cl3 HCl
CHCl3 Cl2 C Cl4
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Dehydrogenation Reactions

• CH3CH3 CH2 CH2

Ethylene
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Cyclic alkanesCnH2n

• A cycloalkane is made of a hydrocarbon chain that
  has been joined to make a ring.

• Note that two hydrogen atoms were lost in forming
  the ring

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Ring Structures
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Cyclohexane - Boat Chair Conformations

• Cyclohexane is NOT a planar molecule. To achieve
  its 109.5 bond angles and reduce angle strain,
  it adopts several different conformations.
• The BOAT and CHAIR (99) are two conformations

Boat
chair
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22.2 Alkenes and Alkynes

• Alkenes hydrocarbons that contain a
  carbon-carbon double bond. CnH2n
• CC Ethene
• C?CC propene
• Alkynes hydrocarbons containing a carbon-carbon
  triple bond. CnH2n-2
• C ?C Ethyne
• C?C?C ? C?C 2-pentyne

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Alkenes Alkynes

• The suffix for the parent alkane chains are
  changed from ane to ene and yne
• e.g. ethene, ethyne
• Where it is ambiguous, the BONDS are numbered
  like branches so that the location of the
  multiple bond may be indicated

• Alkenes are hydrocarbons that contain at least
  one carbon-carbon double bond
• Alkynes are hydrocarbons that contain at least
  one carbon-carbon triple bond

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Alkenes, CnH2n

• Cycle formation isnt the only possible result of
  dehydrogenation.
• Adjacent Cs can double bond, CC, making an
  (unsaturated) alkene.

Sp2
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Nomenclature for Alkenes

• 1. Parent hydrocarbon name ends in -ene
• C2H4 CH2CH2 is ethene
• 2. With more than 3 carbons, double bond is
  indicated by the lowest numbered carbon atom in
  the bond.
• CC-C?-C is 1-butene

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Nomenclature alkenes and alkynes
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Cis and Trans Isomers

• Double bond is fixed (rotation around the double
  bond is restricted)
• Cis/trans Isomers are possible
• CH3 CH3 CH3
• CH CH CH CH
• cis trans CH3

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Reactions of alkenes and alkynes
1. Addition Reactions

• in which (weaker) ? bonds are broken and new
  (stronger) ? bonds are formed to atoms being
  added.

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Hydrogenation reaction

• Adds a hydrogen atom to each carbon atom of a
  double bond
• H H H H
• catalyst
• HCCH H2 HCCH
• H H
• Ethene Ethane

CH3-CH3
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Halogenation reaction

• Adds a halogen atom to each carbon atom of a
  double bond
• H H H H
• catalyst
• HCCH Cl2 HCCH
• Cl Cl
• Ethene Dichloro ethane

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Halogenation Reactions
CH2 CHCH2CH2CH2 Br2

CH2Br CHBrCH2CH2CH2

1,2-dibromopentane
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Alkynes, CnH2n2

• sp triple bonding makes a rigid 180 segment in a
  hydrocarbon.

• Carbon-carbon triple bonds
• Names end in -yne
• HC?CH ethyne(acetylene)
• HC?C-CH3 propyne

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The Bonding in Acetylene
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Naming Alkenes and Alkynes

• When the carbon chain has 4 or more C atoms,
  number the chain to give the lowest number to
  the double or triple bond.
• 1 2 3 4
• CH2CHCH2CH3 1-butene
• CH3CHCHCH3 2-butene
• CH3CH?CHCH3 2-butyne

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Question

• Write the IUPAC name for each of the following
  unsaturated compounds
• A. CH3CH2C?CCH3
• CH3
• B. CH3CCHCH3 C.

2-pentyne
2-methyl-2-butene
3-methylcyclopentene
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Question

• Name the following compound

5-ethyl-3-heptyne
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Additions reactionsHydrogenation and Halogenation

• Hydrogens and halogens also add to the triple
  bond of an alkyne.

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22.3 Aromatic hydrocarbonsUnsaturated Cyclic
hydrocarbons

• Alternating single/double bond
• cycles occur in many organic molecules
• This class is called aromatic (by virtue of
  their aroma).

• Delocalized ? bonds
• possess a great stability
• thus benzene does not
• react like unsaturated
• hydrocarbons

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Benzene C6H6

• The ? structure is often preserved in benzene
  chemical reactions
• Aromatic rings do not add, they substitute
  instead

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Shorthand notation for benzene rings
The bonding in the benzene ring is a combination
of different Lewis structures
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Aromatic Hydrocarbons

• Substitution reaction

Nitroobenzene
Chlorobenzene
-NO2
-CH3
Cl2
Toluene
HNO3
HNO3
benzene
CH3Cl
HCl H2O HCl
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Nomenclature of benzene derivatives
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More Complex Aromatic Systems
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22.4 Hydrocarbon Derivatives(Functional Groups)

• Molecules that are fundamentally hydrocarbons but
  have additional atoms or group of atoms called
  functional groups
• Part of an organic molecule where chemical
  reactions take place
• Replace an H in the corresponding alkane
• Provide a way to classify organic compounds

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The Common Functional Groups

• Class General Formula
• Halohydrocarbons R?X
• Alcohols R?OH
• Ethers R?O?R?
• Aldehydes

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• Class General Formula
• Ketones
• Carboxylic Acids
• Esters
• Amines

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Some Types of Functional Groups

• Haloalkane -F, -Cl, -Br CH3Cl
• Alcohol -OH CH3OH
• Ether -O- CH3-O-CH3
• Aldehyde
• Ketone

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More Functional Groups

• Carboxylic acid -COOH CH3COOH
• Ester -COO- CH3COOCH3
• Amine -NH2 CH3NH2
• Amide -CONH2 CH3CONH2

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Haloahydrocarbons

• An alkane in which one or more H atoms is
  replaced with a halogen (F, Cl, Br, or I)
• CH3Br bromomethane
• Br (methyl bromide)
• CH3CH2CHCH3 2-bromobutane
• Cl
• chlorocyclobutane

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• Name the following
• bromocyclopentane
• 1,3-dichlorocyclohexane

1
2
3
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Substituents

• List other attached atoms or groups in
  alphabetical order
• Br bromo, Cl chloro
• Cl Br
• CH3CHCH2CHCH2CH2CH3
• 4-bromo-2-chloroheptane

5
3
2
4
1
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Nomenclature

• The name of this compound is
• Cl CH3
• CH3CH2CHCH2CHCH3
• 4-chloro-2-methylhexane

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Alcohols ROH

• The OH makes alcohol polar enough to hydrogen
  bonding
• Thus, they are water soluble
• Ethanol is produced by the fermentation of
  glucose

C6H12O6 Glucose
2CH3CH2OH Ethanol
2 CO2

• Methanol is produced industrially by
  hydrogenation
• of carbon monoxide

CO 2H2O CH3OH
Methanol
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Uses of alcohols

• Methanol is used to synthesize adhesives, fibers,
  plastics and recently as motor fuel
• It is toxic to human and can lead to blindness
  and death
• Ethanol can be added to gasoline to form gasohol
  and used in industry as solvent
• Commercial production of ethanol
• CH2CH2 H2O CH3CH2OH

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Classes of alcohols
Alcohols can be classified according to the
number of hydrocarbon fragments bonded to the
carbon where the OH group is attached
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Naming Alcohols

• In IUPAC name, the -e in alkane name is replaced
  with -ol.
• CH4 methane
• CH3OH methanol (methyl alcohol)
• CH3CH3 ethane
• CH3CH2OH ethanol (ethyl alcohol)

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Phenol (Aromatic alcohol)
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Some Typical Alcohols

• OH
• Rubbing alcohol CH3CHCH3
• 2-propanol (isopropyl alcohol)
• Antifreeze HO-CH2-CH2-OH
• 1,2-ethanediol (ethylene glycol)

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Naming Alcohols

• IUPAC names for longer chains number the chain
  from the end nearest the -OH group.
• CH3CH2CH2OH 1-propanol
• OH
• CH3CHCH3 2-propanol
• CH3 OH
• CH3CHCH2CH2CHCH3 5-methyl-2-hexanol

5
2
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Example

• Name the following alcohols
• OH
• CH3CHCHCH2CH3
• CH3

3-methyl-2-pentanol
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Aldehydes and Ketones

• In an aldehyde, an H atom is attached to a
  carbonyl group
• O carbonyl group
• ?
• CH3-C-H
• In a ketone, two carbon groups are attached to a
  carbonyl group
• O carbonyl group
• ?
• CH3-C-CH3

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Naming Aldehydes

• IUPAC name Replace the -e in the alkane name
  by -al
• Common Add aldehyde to the prefixes form (1C),
  acet (2C), propion(3), and butry(4C)
• O O O
• ? ? ?
• H-C-H CH3-C-H CH3CH2C-H
• methanal ethanal propanal
• (formaldehyde) (acetaldehyde)
  (propionaldehyde)

methane
propane
ethane
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Aldehydes as Flavorings
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Naming Ketones

• IUPAC name the -e in the alkane name is replaced
  with one and a number to indicate the position
  of carbonyl group when needed.
• In the common name, add the word ketone
• after naming the alkyl groups attached to the
  
• carbonyl group
• O O
• ? ?
• CH3 -C-CH3 CH3-C-CH2-CH3
• 2-Propanone 2-Butanone
• (Dimethyl ketone) (Ethyl methyl ketone)

butane
propane
cyclohexane
Acetone
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Name the following compounds

• O
• ?
• A. CH3CH2CCH3 B.
• 2-butanone (ethyl methyl ketone)
• CH3 O
• ?
• C. CH3-C-CH2CH
• cyclohexanone
• CH3
• 3,3-dimethylbutanal

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Draw the structural formulas for each of the
following compounds

• CH3 O
  ?
• A. 3-Methylpentanal CH3CH2CHCH2CH
• Br O
• ?
• B. 2,3-Dibromopropanal Br-CH2CHCH
• 
  O
• ?
• C. 3-Methyl-2-butanone CH3CHCCH3
• CH3

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Preparation of aldehydes and Ketones

• They are produced by oxidation of alcohols
• CH3CH2OH

Oxidation
acetaldehyde
ethanal
Primary alcohol
Oxidation
acetone
propanone
Secondary alcohol
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Carboxylic Acids and Esters

• Carboxylic acids contain the carboxyl group as
  carbon 1.
• O
• R ??
• CH3 COH CH3COOH
• carboxyl group
• General formula RCOOH

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Nomenclature of Carboxylic Acids

• Formula IUPAC Common
• alkan -oic acid prefix ic acid
• HCOOH methanoic acid formic acid
• CH3COOH ethanoic acid acetic acid
• CH3CH2COOH propanoic acid propionic acid
• CH3CH2CH2COOH butanoic acid butyric acid

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IUPAC nomenclature for Carboxylic acids

• Identify longest chain
• Number carboxyl carbon as 1
• CH3
• CH3 CHCH2 COOH
• 3-methylbutanoic acid

1
4
2
3
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• CH3
• CH3CHCOOH
• 2-methylpropanoic acid

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Reaction of carboxylic acid with alcohol
Esterification
Alcohol
Carboxylic acid
Ester
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Esters

• In ester, the H in the carboxyl group is replaced
  with an alkyl group
• O
• ??
• CH3 CO CH3 CH3COO CH3
• ester group

• Esters give fruity odors

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Naming Esters

• The parent alcohol is named first with a yl
  ending
• Change the oic ending of the parent acid to
  ate
• acid alcohol
• O
• ?? methyl
• CH3 CO CH3
• Ethanoate methyl ethanoate (IUPAC)
• (acetate) methyl acetate (common)

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Amines

• Organic compounds of nitrogen N derivatives of
  ammonia
• Classified as primary, secondary, tertiary
• CH3 CH3
• ? ?
• CH3NH2 CH3NH CH3N CH3
• Primary Secondary Tertiary
  
• one N-C two N-C three N-C
• bond bonds bonds

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Naming Amines

• IUPAC aminoalkane Common alkylamine
• CH3CH2NH2
• aminoethane
• (ethylamine)
• NH2
• CH3CHCH3
• 2-aminopropane Aniline
• (isopropylamine)

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22.5 PolymersPoly many mersparts

• Polymers are large, usually chainlike molecules
  that are built from small molecules called
  monomers joined by covalent bonds
• Monomer Polymer
• Ethylene Polyethylene
• Vinyl chloride Polyvinyl chloride
• Tetrafluoroethylene Teflon

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Some common synthetic polymers, their monomers
and applications
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Types of Polymerization

• Addition Polymerization monomers add together
  to form the polymer, with no other products. (
  Polyethylene and Teflon)
• Condensation Polymerization A small molecule,
  such as water, is formed for each extension of
  the polymer chain. (Nylon)

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Addition Polymerization
A species with an unpaired electron such as
hydroxyl free radical
The polymerization process Is initiated by a free
radical
Free radical attacks and break The ? bond of
ethylene molecule To form a new free radical

• Repetition of the process thousands of times
  creates a long chain
• polymer
• The process is terminated when two radicals
  react to form a bond
• thus there will be no free radical is
  available for further repetitions.

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Condensation PolymerizationFormation of Nylon
Dicarboxylic acid
Diamine
Dimer

• Small molecule such as H2O is formed
• from each extension of the polymer chain
• both ends are free to react

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Nylon