1
Organic and Biological Organic and Biological MoleculesMolecules
Chapter 22Chapter 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 of rings
of carbon atoms.
•The study of the chemistry of living
matter
3
Hydrocarbons• compounds composed of carbon and
hydrogen.
• Saturated compounds (alkanes) have the maximum number of hydrogen atoms attached to each carbon atom
• Saturated: carbon-carbon bonds are all single - alkanes [CnH2n+2]
H C
H
H
C
H
H
H
4
Unsaturated compounds have fewer hydrogen atoms attached to the carbon chain than alkanes
• Unsaturated: They contain carbon-carbon multiple bonds (double or triple)
H C
H
H
C
H
CH
H
5
22.1 Alkanes: Saturated hydrocarbons
• Saturated hydrocarbons, CnH2n+2
– “Saturated” because they can’t take any more hydrogen atoms
– Straight chains are H3C–(CH2)n–2–CH3
– Waxes, oils, & fuel gases as n decreases.
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Alkanes: Saturated Hydrocarbons
• Hydrocarbons are molecules composed of carbon & hydrogen– Each carbon atom forms 4 chemical bonds– A saturated hydrocarbon is one where all C - C bonds are
“single” bonds & the molecule contains the maximum number of H-atoms
– Saturated hydrocarbons are called ALKANES
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Methane is a tetrahedral molecule
8
The Lewis structure of ethane.
9
A ball-and-stick model of ethane.
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Propane
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Butane
12
The First 10 “Normal” AlkanesNameName FormulaFormula M.P.M.P. B.P.B.P. # Structural Isomers# 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 C1 - C4 are Gases at Room Temperatureat Room Temperature
C5 - C16 are Liquids C5 - C16 are Liquids at Room Temperatureat Room Temperature
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The C-H Bonds in Methane
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IUPAC Rules for Naming Branched Alkanes
• Find and name the parent chainFind and name the parent chain in the hydrocarbon - this forms the root of the hydrocarbon name
• Number the carbon atoms in the parent chainNumber the carbon atoms in the parent chain starting at the end closest to the branching
• Name alkane branchesName 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 alphabeticallyalphabetically
• Finally, use prefixesuse 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 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
CH3
CH2CH2
CH2CH3
CH3
CH2CH
CH3
CH3
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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.
CH3
CH2CH2
CH2CH3
CH3
CH2CH
CH3
CH3
n-pentane, C5H12
2-methlbutane, C5H12
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Isomer Naming• Older conventions would have that
as “isooctane,” but a good IUPAC name results from the following:– Name the longest C chain (pentane)– List the side groups in alphabetical
order with Greek prefixes (trimethylpentane)
– Supply (smallest possible) positional indices (2,2,4 trimethylpentane)
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Example : Show the structural formula of 2,2-dimethylpentane2,2-dimethylpentane
• The parent chain is indicated by the ROOT of the name - “pentanepentane”. This means there are 5 carbons in the parent chain.
CH3
CH2CH2
CH2CH3
• “dimethyldimethyl” tells us that there are TWO methyl branches on the parent chain. A methyl branch is made of a single carbon atom.
• “2,22,2-” tell us that BOTH methyl branches are on the second carbon atom in the parent chain.
CH31
CCH23
CH2
4
CH35
CH3
CH3
1
2
3
4
5
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Example: Structural formula of 3-ethyl-2,4-dimethylheptane?3-ethyl-2,4-dimethylheptane?
• The parent chain is indicated by the ROOT of the name - “heptaneheptane”. This means there are 7 carbons in the parent chain.
CH3
CH2CH2
CH2CH2
CH2CH3
• “2,4-dimethyl2,4-dimethyl” tells us there are TWO methyl branches on the parent chain, at carbons #2 and #4.
• “3-ethyl3-ethyl-” tell us there is an ethyl branch (2-carbon branch) on carbon #3 of the parent chain.
1
2
3
4
5
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CH3
CHCH
CHCH2
CH2CH3
CH2
CH3
CH3 CH3
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Example: 2,3,3-trimethyl-4-propyloctane2,3,3-trimethyl-4-propyloctane
• The parent chain is indicated by the ROOT of the name - “octaneoctane”. This means there are 8 carbons in the parent chain.
• “2,3,3-trimethyl2,3,3-trimethyl” tells us there are THREE methyl branches - one on carbon #2 and two on carbon #3.
• “4-propyl4-propyl-” tell us there is a propyl branch (3-carbon branch) on carbon #4 of the parent chain.
1
2
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5
7
6
8
1
23
45
7
6
8
CHC
CHCH2
CH2
CH2CH3
CH3
CH3
CH3
CH3CH2
CH2
CH3
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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-dimethylpentane2,3-dimethylpentane
CH3
CH2
CHCH
CH3
CH3
CH3
• parent chain has 8 carbons - “octane”
• two methyl branches - start counting from the left - #3 and #4
• one ethyl branch - #5
• name branches alphabetically
3,4-dimethyl3,4-dimethyl
4433
octaneoctane
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5-ethyl-5-ethyl-
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Reactions of alkanes
• Combustion reactions
2C4H10 + 13 O2 8CO2 + 10 H2O(g)
• Substitution ReactionsSubstitution Reactions
CHCl Cl CCl HClh3 2 4
CH4 + Cl2 CH3Cl + HCl
CH3Cl + Cl2 CH2Cl2 + HCl
CH2Cl2 + Cl2 CH Cl3 + HCl
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Dehydrogenation ReactionsDehydrogenation Reactions
CH3CH3 CH2 CH2
Ethylene
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Cyclic alkanesCyclic alkanes
• A cycloalkane is made of a hydrocarbon chain that has been joined to make a “ring”.
CH3
CH2
CH3 CH2
CH2
CH2
n-propaneC3H8
cyclopropaneC3H6
60° bond angleunstable!!
109.5° bond angle
•Note that two hydrogen atoms were lost in forming the ring
•What is the general formula for a cycloalkane?
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Cyclic alkanes, CnH2n
• If the two end C’s lose 1 H each, they have free valence to close a ring
• Again, properties similar to straight chains.– Can now have conformational
isomers!
– E.g., BOAT cyclohexane versus CHAIR
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Cyclohexane - Boat & Chair Conformations
• Cyclohexane is NOT a planar molecule. To achieve To achieve its 109.5° bond angles and reduce angle strainits 109.5° bond angles and reduce angle strain, it adopts several different conformations.
• The BOATBOAT and CHAIRCHAIR (99%) are two conformations
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Unsaturated hydrocarbomns22.2 Alkenes and Alkynes
Alkenes: hydrocarbons that contain a carbon-carbon double bond. [CnH2n]
C=C Ethene
CC=C propene
Alkynes: hydrocarbons containing a carbon-carbon triple bond. [CnH2n-2]
C C Ethyne
CCCCC 2-pentyne
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Alkenes & AlkynesAlkenes & Alkynes
• Alkenes are hydrocarbons that contain at least one one carbon-carboncarbon-carbon double bonddouble bond
• Alkynes are hydrocarbons that contain at least one one carbon-carboncarbon-carbon triple triple bondbond
• 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 the location of the multiple location of the multiple bond may be indicatedbond may be indicated
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Alkenes, CnH2n
• Cycle formation isn’t the only possible result of dehydrogenation.
• Adjacent C’s can double bond, C=C, making an (unsaturated) alkene.
Sp2
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The Bonding in Ethylene
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Nomenclature for Alkenes
1.Root hydrocarbon name ends in -ene
C2H4; CH2=CH2 is ethene
2.With more than 3 carbons, double bond is indicated by the lowest by the lowest numbered carbonnumbered carbon atom in the bond.
C=CCC is 1-butene
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Alkene Isomers
• While an sp3 CX2Y2 has only 1 isomer,• (every X and Y is adjacent to all the others)
• the sp2 alkene C2X2Y2 has cis & trans isomers (where X is or isn’t on the same side of = as X).
– For longer hydrocarbons, cis & trans refer to the side the chain extends:
CXX
YY
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Cis and Trans Isomers
Double bond is fixed Cis/trans Isomers are possible
CH3 CH3 CH3
CH = CH CH = CH
cis trans CH3
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Addition Reactions
• Weaker bonds are broken and new (stronger) bonds are formed to atoms being added.
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Hydrogenation
Adds a hydrogen atom to each carbon atom of a double bond
H H H H
Ni
H–C=C–H + H2 H–C–C–H
H H
ethene ethane
CHCH33-CH-CH33
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Halogenation
Adds a halogen atom to each carbon atom of a double bond
H H H H
Ni
H–C=C–H + Cl2 H–C–C–H
Cl Cl
ethene dichloro ethane
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Halogenation Reactions
CH2 CHCH2CH2CH2 + Br2
CH2Br CHBrCH2CH2CH2
1,2-dibromopentane
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Alkynes, CnH2n–2
Carbon-carbon triple bonds Names end in -yne
HCCH ethyne(acetylene)
HCC-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
CH2=CHCH2CH3 1-butene
CH3CH=CHCH3 2-butene
CH3CHCHCH3 2-butyne
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Question
Write the IUPAC name for each of the following unsaturated compounds:
A. CH3CH2CCCH3
CH3
B. CH3C=CHCH3
2-pentyne
2-methyl-2-butene
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Question
• Name the following compound
CH3CH2C CCHCH2CH3CH2CH3
CH3CH2C CCHCH2CH3CH2CH3
1 2 3 4 5 6 7
5-ethyl-3-heptyne
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Additions reactions:Hydrogenation and Halogenation
Hydrogens and halogens also add to the triple bond of an alkyne.
CH3C CCH2CH3 + Br2 CH3C CCH2CH3
Br Br
Br Br
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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).– The structure is often preserved in
their chemical reactions; they don’t add, they substitute instead.
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Lewis structures for the benzene ring.
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Benzene C6H6
sp2
sp2sp2
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Shorthand notation for benzene rings
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The bonding in the benzene ring is a combination of different Lewis structures.
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Aromatic Hydrocarbons
Substitution reaction
+ Cl2
FeCl3
Cl
+ HCl+H2O+HCl
benzene
Chlorobenzene
HNO3
HNO3
CH3Cl
-NO2
-CH3
Nitroobenzene
Toluene
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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 RX Alcohols ROH
Ethers ROR
AldehydesR C
O
H
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Class General Formula
Ketones
Carboxylic Acids
Esters
Amines
R C
OR'
R C
OOH
R C
OOR'
R NH2
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Some Types of Functional Groups
Haloalkane -F, -Cl, -Br CH3Cl
Alcohol -OH CH3OH
Ether -O- CH3-O-CH3
Aldehyde
Ketone
C H
OCH3CH
O
C
O
CH3CCH3
O
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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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Nomenclature
Name the following:
bromocyclopentane
1,3-dichlorocyclohexane
Br
Cl
Cl
1 2 3
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Substituents
List other attached atoms or groups in alphabetical orderBr = bromo, Cl = chloro
Cl Br
CH3CHCH2CHCH2CH2CH3
4-bromo-2-chloroheptane
1 2 3 4 5
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Nomenclature
The name of this compound is:
Cl CH3
CH3CH2CHCH2CHCH3
1) 2,4-dimethylhexane
2) 4-chloro-5-methylhexane
3) 4-chloro-2-methylhexane
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Solution
The name of this compound is:
Cl CH3
CH3CH2CHCH2CHCH3
3. 4-chloro-2-methylhexane
123456
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Alcohols: R–OH • The –OH makes alcohol polar enough
to hydrogen bondhydrogen bond.
• Thus, they are water solublewater soluble
• Ethanol is a fermentation product acid.
yeastC6H12O6
Glucose2CH3CH2OHEthanol + 2 CO2
CO + 2H2O CH3OH Methanol
• Methanol is produced industrially by hydrogenation of carbon monoxide
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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:
CH2=CH2 + H2O CH3CH2OH
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Classes of alcohols
R CH2OH Primary alchol
CHOHR'R
Secondary alcohol
CR'R
R"OH Tertiary alcohol
Alcohols can be classified according to the number number of hydrocarbon fragments bonded to the carbonof 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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OH
Phenol(Aromatic alcohol)
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More Names of Alcohols
IUPAC names for longer chains number the chain from the end nearest the -OH groupend nearest the -OH group.
CH3CH2CH2OH 1-propanol
OH CH3CHCH3 2-propanol
CH3 OH CH3CHCH2CH2CHCH3 5-methyl-2-hexanol
5 2
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Some Typical Alcohols
OH
“Rubbing alcohol” CH3CHCH3
2-propanol (isopropyl alcohol)
Antifreeze HO-CH2-CH2-OH
1,2-ethanediol1,2-ethanediol (ethylene glycol)
OH
glycerol HO-CH2-CH-CH2OH
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Name the following alcohols:A. OH
CH3CHCHCH2CH3
CH3
OHB.
Example
3-methyl-2-pentanol
Cyclobutanol
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Reactions of Alcohols
Combustion
CH3OH + 2O2 CO2 + 2H2O + Heat
Dehydration
H OH heat
H-C-C-H H-C=C-H + H2O
H H H H
alcohol alkene
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Ethers
• Contain an -O--O- between two carbon groups• Simple ethers named from -yl names-yl names of the
attached groups and adding adding etherether.
CH3-O-CH3 dimethyl ether
CH3-O-CH2CH3 ethyl methyl ether
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Aldehydes and Ketones
In an aldehyde, an H atomH atom is attached to a carbonyl group
O carbonyl group CH3-C-H
In a ketone, two carbon groupstwo carbon groups are attached to a carbonyl group
O carbonyl group CH3-C-CH3
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Naming Aldehydes
IUPAC Replace the -e in the alkane name -alCommon 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)
methaneethane propane
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Aldehydes as Flavorings
CH
O
CH
O
HO
OCH3
CH=CH CH
O
Benzaldehyde Vanillin Cinnamaldehyde(almonds) (vanilla beans) (cinnamon)
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Naming Ketones
In the IUPAC name, the -e in the alkane name is replaced with -one
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
Propanone 2-Butanone
(Dimethyl ketone) (Ethyl methyl ketone)
O
Cyclohexanone
Acetone
propane butane
cyclohexane
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Preparation of aldehydes and Ketones
They are produced by oxidation of alcohols:
CH3CH2OHOxidation
CH3CHCH3
OH
Oxidation CH3CCH3O
CH3CO
Hacetaldehyde
acetone
Primary alcohol
Secondary alcohol
ethanal
propanone
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Question
Classify each as an aldehyde (1), ketone (2) or neither(3).
O
A. CH3CH2CCH3 B. CH3-O-CH3
CH3 O
C. CH3-C-CH2CH D.
CH3
O
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Solution
Classify each as an aldehyde (1), ketone (2) or neither(3).
O
A. CH3CH2CCH3 2 B. CH3-O-CH3 3
CH3 O
C. CH3-C-CH2CH 1 D. 2
CH3
O
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Question
Name the following
O
A. CH3CH2CCH3 B.
CH3 O
C. CH3-C-CH2CH
CH3
O
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Solution
O
A. CH3CH2CCH3 B.
2-butanone (ethyl methyl ketone)
CH3 O
C. CH3-C-CH2CH cyclohexanone CH3
2,2-dimethylbutanal
O
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Question
Draw the structural formulas for each:
A. 3-Methylpentanal
B. 2,3-Dichloropropanal
C. 3-Methyl-2-butanone
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Solution
Draw the structural formulas for each: 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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Carboxylic Acids and Esters Carboxyl Group
Carboxylic acids contain the carboxyl group as carbon 1.
O
R CH3 — C—OH : CH3—COOH
carboxyl group
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Naming 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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Naming Rule for Carboxylic acids
• Identify longest chain
• (IUPAC) Number carboxyl carbon as 1carboxyl carbon as 1
CH3
|
CH3 — CH—CH2 —COOH
IUPAC 3-methylbutanoic acid
1234
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Question
Give IUPAC name:
A. CH3COOH
CH3
|
B. CH3CHCOOH
2
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Solution
A. CH3COOH
ethanoic acid; acetic acid
CH3
|
B. CH3CHCOOH
2-methylpropanoic acid;
93
Preparation of carboxylic acids
• Oxidation of primary alcohols
CH3CH2OH CH3COOHKMnO4
94
Reaction of carboxylic acid with alcohol
CH3CO
OH + H OCH2CH3
CH3CO
OCH2CH3 + H2O
Ester
Carboxylic acid Alcohol
Esterification
95
Esters
In a ester, the H in the carboxyl group is replaced with an alkyl group
O
CH3 — C—O —CH3 : CH3—COO —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 — C—O —CH3
Ethanoate methyl ethanoate (IUPAC)(acetate) methyl acetate (common)
97
Some esters and their names
Flavor/Odor
Raspberries
HCOOCH2CH3 ethylmethanoate
(IUPAC)
ethylformate (common)
Pineapples
CH3CH2CH2 COOCH2CH3
ethylbutanoate (IUPAC)
ethylbutyrate (common)
98
Question
Give the IUPAC and common names of the following compound, which is responsible for the flavor and odor of pears.
O
CH3 — C— O —CH2CH2CH3
99
Solution
O propyl
CH3 — C—O —CH2CH2CH3
propylethanoate (IUPAC)
propyl acetate (common)
100
Question
Draw the structure of the following compounds:
A. 3-bromobutanoic acid
B. Ethyl propionoate
101
Solution
A. 3-bromobutanoic acid
Br
|
CH3CHCH2COOH
B. Ethyl propionoate O
CH3 CH2 COCH2CH3 CH3CH2COOCH2CH3
102
Hydrolysis of esters
• Esters react with water and acid catalyst• Split into carboxylic acid and alcohol
O H+
H — C—O—CH2CH3 + H2O
O
H — C—OH + HO—CH2CH3
-OHH
103
Amines
• Organic compounds of nitrogen N; derivatives of ammonia
• Classified as primary, secondary, tertiary
CH3 CH3
CH3—NH2 CH3—NH CH3—N — CH3
Primary Secondary Tertiary
one N-C two N-C three N-Cbond bonds bonds
104
Naming Amines
IUPAC aminoalkane Common alkylamine
CH3CH2NH2 CH3—NH —CH3
aminoethane N-methylaminomethane(ethylamine) (dimethylamine)
NH2
|
CH3CHCH3
2-aminopropane Aniline N-methylaniline(isopropylamine)
NH2 NH CH3
105
Question
Give the common name and classify:
A. CH3NHCH2CH3
CH3
|
B. CH3CH2NCH3
106
Solution
A. CH3NHCH2CH3
ethylmethylamine, (Secondary)
CH3
|B. CH3CH2NCH3
ethyldimethylamine, (Tertiary)
107
Question
Write a structural formula for
A. 2-aminopentane
B. 1,3-diaminocyclohexane
108
Solution
A. 1-aminopentane
CH3CH2CH2CH2CH2-NH2
B. 1,3-diaminocyclohexane
NH2
NH2
109
PolymersPoly= many; mers=parts
• Polymers are large, usually chainlike molecules that are built from small molecules called monomers joined by covalent bonds
Monomer PolymerEthylene PolyethyleneVinyl chloride Polyvinyl
chlorideTetrafluoroethylene Teflon
110
111
Some common synthetic polymers, their monomers and applications
112
Types of Polymerization
Addition Polymerization:Addition Polymerization: monomers “add together” to form the polymer, with no other products. (Teflon)
Condensation Polymerization:Condensation Polymerization: A small molecule, such as water, is formed for each extension of the polymer chain. (Nylon)
113
Addition Polymerization
OH
C CH
H
H
HCOH
H CH
H
H
C CH
H
H
H
COH
H CH
H
H
COH
H CH
H
HC CH H
H H
The polymerization processIs initiated by a free radical
A species with an unpaired electron such as hydroxyl free radical
Free radical attacks and breakThe bond of ethylene moleculeTo 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.
114
• Depending upon conditions of polymerization, the product may be branched branched or linearlinear polyethylene
(Polythene)
another
115
116
117
118
119
120
121
Condensation PolymerizationFormation of Nylon
NH
H(CH2)6 N
H
H CO
O(CH2)4H
CO
O H
Hexamethylendiamine Adipic acid
NH
H(CH2)6 N
HC (CH2)4 C
O
O H
O+ H2O
• Small molecule such as H2O is formed from each extension of the polymer chain• both ends are free to react
Dimer
Diamine Dicarboxylic acid
122
NH
(CH2)6 NH
( C (CH2)4 COO
)n
Nylon
123
124
Proteins
• Natural polymers made up of -amino
acids (molecular weight from 6000 to
>1,000,000 g/mol).
1. Fibrous Proteins: provide structural integrity and strength to muscle, hair and cartilage.
125
Proteins
2. 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
126
-Amino Acids
NH2 always attached to the -carbon (the carbon attached to COOH)
•C = -carbon
H2N C
H
COOH
R
127
Bonding in -Amino Acids
• + H2O
•
A peptide linkage (amide group)
•There are 20 amino acids commonly found in proteins.• Additional condensation reaction produces polypeptide eventually yielding a protein
CNH
H
H
R
C
O
N
H
C
H
R'
CO
OHDipeptide
• The protein polymer is built by condensation reaction between amino acids
128
The 20 Alpha-amino Acids found in most proteins
129
Levels of Structure•Primary: Sequence of amino acids in the protein chain. (lycine-alanine-leucne: (lys-ala-leu).
– So many arrangements can be predicted.
Tripeptide containing Glycine, Cysteine, and Alanine
130
Levels of Structure
•Secondary: The arrangement of the protein chain in the long molecule (hydrogen bonding determines this).
• Hydrogen bonding between lone pairs on an oxygen atom in the carbonyl group of an amino acid and a hydrogen atom attached to a nitrogen of another amino acid
C O NH
This type of interaction can occur with the chain coils to form a spiral structure called - helix- helix
131
Hydrogen bonding within a protein chain causes it to form a stable helical structure called the alpha-Helix
This is found infibrous protein likewool and hair givingit the elasticity
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•Tertiary: The overall shape of the protein (determined by hydrogen-bonding, dipole-dipole interactions, ionic bonds, covalent bonds and London forces).
Summary of the Various Types of Interactions that Stabilize the Tertiary Structure of a Protein: (a) Ionic, (b) Hydrogen Bonding, (c) Covalent, (d) London Dispersion, and (e) Dipole-Dipole
133
Summary of the Various Types of Interactions that Stabilize the Tertiary Structure of a Protein: (a) Ionic, (b) Hydrogen Bonding, (c) Covalent, (d) London Dispersion, and(e) Dipole-Dipole
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CarbohydratesCarbohydrates
Food source for most organisms and structural material for plants.Empirical formula = (CH2O)n
Most carbohydrates such as starch and cellulose are polymers of monosacharides or polymers of monosacharides or simple sugar monomerssimple sugar monomersMonosaccharides (simple sugars) are polyhydroxy ketones and aldehydes
Pentoses (5-carbon atoms) - ribose, arabinoseHexoses (6-carbon atoms) - fructose, glucose
135
Some Important Monosaccharides
136
Chiral carbon atoms in fructose
• Molecules with nonsuperimposable mirror images exhibit optical isomerism
• A carbon atom with different groups bonded to it in a tetrahedral arrangement always has a nonsuperimposable mirror images which gives rise to a pair of optical isomers
137
Tetrahedral Carbon atom with four different substituents cannot have its mirror image superimposed
138
The Mirror Image Optical Isomers of Glyceraldehyde
*Chiral carbonatom
139
Fructose
D-Fructose
H2OHC
C
CHO H
C
O
H OH
C
CH2OH
OHH
*
*
*
There are 3 chiralCarbon atomsThere are 23 isomersThat differ in the abilityTo rotate light
140
Complex carbohydrates
Disaccharides (formed from 2 monosaccharides joined by a glycoside linkage)
sucrose (glucose + fructose)
Polysaccharides (many monosaccharide units)
starch, cellulose
141
Sucrose is a disaccharideformed from alpha-D-glucose and fructose
142
)a (The Polymer Amylose is a Major Component of Starch and is Made Up of Alpha-D-Glucose Monomers (b) The Polymer Cellulose, which Consists of Beta-D-Glucose Monomers
143
Nucleic Acids
• Life is possible because each cell when it divides can transmit the vital information about how it works to the next generation
• The substance that stores and transmits information is a polymer called deoxyribonucleic acid (DNA)
• DNA together with other similar nucleic acids called ribonucleic acids is responsible for the synthesis of various proteins needed by the cell to carry out its life functions
144
Nucleic Acids
• DNA (deoxyribonucleic acids): stores and transmits genetic information, responsible (with RNA) for protein synthesis. (Molar mass = several billion)
•RNA (ribonucleic acid): helps in protein synthesis. (Molecular weight = 20,000 to 40,000)
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Monomers of nucleic acidNucleotides
1. Five-carbon sugar, deoxyribose in DNA and ribose in RNA.
2. Nitrogen containing organic base
3. Phosphoric acid molecule, H3PO4
• The base and the sugar combine to form a unit that in turn reacts with phosphoric acid to create a nucleotide• The nucleotides become connected through condensation reaction that eliminate water to give a polymer that contain a billion units.
146
The Organic Bases Found in DNA and RNA
147
The base and sugar combine to form a unit that in turn reacts with phosphoric acid to create the nucleotide, which is an ester
148
A Portion of a typical nucleic acid chain
149
Double helix formation
• According to Watson and Crick (Nobel prize winners), CAN is composed of two strands (threads) running in opposite directions that are bridged by hydrogen bonds between specific pyrimidine groups on one strand and purine group on the other
• The two strands are twisted into a double -helix structure
• The strongest hydrogen bonds form between adonine and thymine and between guanine and cystosine. Thus; A-T or G-C bonding interactions will take place
• The sequence of nucleotides on one strand of the double helix determines the sequence of the other
• The sequence of the bases determines what information is stored.
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)a (The DNA double helix contains two sugar-phosphate backbones, with the bases from the two strands hydrogen bonded to each other; the complementarity of the (b) thymine-adenine and (c) cytosine-guanine pairs
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Genetic Code and Protein Synthesis follows!!!!!!!!!!!