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Organic and Biological Molecules
Chapter 22
Chapter 22 PreviewOrganic and Biological Molecules
Alkanes: Saturated Hydrocarbons Isomerism, Nomenclature, Reactions of alkanes, Cyclic alkanes
Alkenes, Alkynes, and Aromatic Hydrocarbons Reaction of alkenes and alkynes
Hydrocarbon DerivativesAlcohols, Aldehydes and ketones, Carboxylic acids and esters, and amines
Polymers and Natural PolymersProperties of polymers, Types of polymers, plymers based on ethylene, Protein, Carbohydrates, and Nucleic Acids
Late 18th century:•Compounds from living organisms - Organic•Compounds from lifeless matter – Inorganic•Organic compounds thought to have ‘vital force’
Ammonium cyanate(from mineral sources)
‘Inorganic’
Urea(from urine)
‘Organic’
Wöhler 1800-1882 ∆
(Heat)
IntroductionWhat is Organic Chemistry?
It is defined as the study of hydrocarbons (compounds of hydrogen and carbon) and their derivatives
Organic chemicals are universal
OrganicOrganicChemicalsChemicals
Biological matter•Plants•Animals•Microbes
Geological matter•Fossil Fuels•Other
Atmosphericand
cosmic matter
Manufacturedproducts
22.1 Alkanes: Saturated HydrocarbonAlkanes CnH2n+2
consist of only carbon and hydrogen bonded by single covalent bonds single
HCH HH
HCH CH
HH
H
HCH CH
HC
H
HH
H
HCH CH
HC
H
HC
H
HH
H
CH3
HCH CH
HC
H
HC
H
HC
H
HH
H
methane ethane propane butane
CH3CH3 CH3CH2CH3 CH3CH2CH2CH3
pentane
CH3CH2CH2CH2CH3
Skeletal structure of only carbon atoms
propane
butane
pentane
C1 – C4 n-alkanes are all gasesMethane main component of natural gas
Propane and butane often stored as compressed gases
n
1
2
3
4
5
6
MolecularFormula
CH4
C2H6
C3H8
C4H10
C5H12
C6H14
Structuralformula
HCH
CCH
HH
H
HH
HCH
CH
HH
CH
HH
HCH
CCH
HC
H
HH
HCH
CCH
HC
H
HH
HCH
CCH
HC
H
HH
H
H
H
HH
H
HCH
HH
H
HCH
HCH
HH
Name
methane
ethane
propane
butane
pentane
hexane
Condensedstructural
formulaCH4
CH3CH3
CH3CH2CH3
CH3CH2CH2CH3
CH3CH2CH2CH2CH3
CH3CH2CH2CH2CH2CH3
Further members of the series
Heptane CH3CH2CH2CH2CH2CH2CH3
Octane CH3CH2CH2CH2CH2CH2CH2CH3
Nonane CH3CH2CH2CH2CH2CH2CH2CH2CH3
Decane CH3CH2CH2CH2CH2CH2CH2CH2CH2CH3
Undecane CH3CH2CH2CH2CH2CH2CH2CH2CH2CH2CH3
Dodecane CH3CH2CH2CH2CH2CH2CH2CH2CH2CH2CH2CH3
Etc., etc.
Isomers are molecules that have the same molecular formula but different structures
Isomerism
Extent of structural isomerism in alkanes
Alkane No. of structural isomersMethane 1Ethane 1Propane 1Butane 2Pentane 3Hexane 5
Decane 75
Pentadecane 4347
Eicosane 366,319
Triacontane 44 x 109(C30H62)
All known
Pentane C5H12 3 structural isomers
CH3 CH2 CH2 CH2 CH3 CH3 CH2 CH CH3
CH3
CH3 C CH3
CH3
CH3
•No other arrangements of C5H12 possible •All of these based on tetrahedral (sp3 hybridised) Carbon
CH3 CH2 CHCH3
CH3 CH3 CH CH2 CH3CH3
CH3 CH2 CHCH3
CH3
= =
Note
etc.
How many structural isomers does pentane, C5H12, have?
C C C C C
H H H H H
H
HHHHH
H
C C C C
H CH3 H H
H
HHHH
H
C C C
H CH3 H
H
HH
H
CH3
n-pentane
2-methylbutane
2,2-dimethylpropane
1. The parent name of the hydrocarbon is that given to the longest continuous chain of carbon atoms in the molecule.
CH3 CH2 CH2 CH CH2 CH2 CH3
CH3
1 2 3 4 5 6 74-methylheptane
2. An alkane minus one hydrogen atom is called an Alkyl group
CH4
CH3
methane
methyl
Common Alkyl Groups
Nomenclature
3. When one or more hydrogen atoms are replaced by other groups, the name of the compound must indicate the locations of carbon atoms where replacements are made. Number in the direction that gives the smaller numbers for the locations of the branches.
CH3 CH CH2 CH2 CH3
CH3
1 2 3 4 5
2-methylpentane
CH3 CH2 CH2 CH CH3
CH3
1 2 3 4 5
4-methylpentane
Nomenclature
4. Use prefixes di-, tri-, tetra-, when there is more than one alkyl branch of the same kind.
CH3 CH CH CH2 CH2 CH3
CH3
1 2 3 4 5 6
CH3
2,3-dimethylhexane
CH3 CH CH CH2 CH2 CH3
CH31 2 3 4 5 6
CH3
3,3-dimethylhexane
Nomenclature
5. Use previous rules for other types of substituents.
CH3 CH CH CH3
Br
1 2 3 4
NO2
2-bromo-3-nitrobutane
CH2 CH CH CH3
Br
1 2 3 4
NO2
1-bromo-3-nitrobutane
Names of Common Groups
Nomenclature
NomenclatureRules for Naming Alkanes:
1. Names after butane are obtained by adding the suffix –ane to the Greek root for the nyumber of carbon atoms (pent- for five, hex- for six …)
2. For a branched carbon hydrocarbons, the name is given for the longest continuous chain
3. When they are substituents, the –ane is replaced with -yl
4. The positions of substituent groups are specified by numbering the longest chain starting from the closest end.
5. The location and names of each substituent are followed by the root alkane name and they have to be listed in alphabetical order, and the prifix di-, tri- … for multiple.
CH3 CH2 CCH3
HCH2 CH2 C
CH3
CH2
CH2 CH3CH2 CH3
CH3 CCH3
CH3
CH2 CCH3
HCH3
2,2,4-Trimethylpentane
CH3 CH2 CCH3
CH2
CH2 CCH3
CH3CH3 H
1
23456
2,4-dimethyl-4-ethylhexane
What is the IUPAC name of the following compound?
1 2 3 4 5 6 7 8CH3 CH CH2 CH CH2 CH2 CH3
C2H5
CH2
CH3
Questions
What is the structure of 2-propyl-4-methylhexane?
Alkane Reactions
CH4 (g) + 2O2 (g) CO2 (g) + 2H2O (l) ∆H0 = -890.4 kJ
Alkanes are fairly uncreative, but at sufficient high temperature react vigorously and exothermically with oxygen
CH4 (g) + Cl2 (g) CH3Cl (g) + HCl (g)light
Cl2 + energy Cl• + Cl•
Cl• + C HH
H
H
C H
H
H
• + HCl
CH
H
H
• + Cl Cl C ClH
H
H
+ Cl•
Combustion reaction
Substitution reaction
Freons CFxCl4-x
Substitution reactionFormation of unsaturated hydrocarbons
CH3CH3 CH2=CH2+H2Using Cr2O3 at high temperature
Cyclic AlkanesAlkanes whose carbon atoms are joined in rings are called Cyclic Alkanes. They have the general formula CnH2n where n = 3,4,…
22.2 Alkene and AlkyneAlkene have the general formula CnH2n where n = 2,3,…
• contain at least one carbon-carbon double bond and the systematic names are ethene, propene, …..
CH2 CH CH2 CH3
1-butene
CH3 CH CH CH3
2-butene
C C
Cl Cl
H H
C C
Cl H
H Clcis-dichloroethylene trans-dichloroethylene
• have restricted rotation around the double bond to produce cis-trans isomerisms
Alkyne
Alkyne have the general formula CnH2n-2 where n = 2,3,4,…
• contain at least one carbon-carbon triple bond and the systematic names are ethyne, propyne, …..
1-butyne 2-butyneCH C CH2 CH3 CH3 C C CH3
Reactions of alkenes and alkynes
Halogenation ReactionsCH2 CH2 (g) + Br2 (g) CH2Br CH2Br (g)
HydrogenationCH CH (g) + H2 (g) CH2 CH2 (g)
PolymerizationSmall molecules are joined together to form large molecules
22.3 Aromatic Hydrocarbons
C
CC
CC
C
H
H
H
H
H
H
C
CC
CC
C
H
H
H
H
H
H
A special class of cyclic unsaturated hydrocarbons
•Benzene is the simplest
•The delocalized p-electronsmake it different thanthe other unsaturated hydrocarbons
•Benzene does not present the addition reactions
Aromatic Compound Nomenclature
CH2CH3
ethylbenzeneCl
chlorobenzene
NH2
aminobenzeneNO2
nitrobenzene
12
34
5
6
Br
Br
1,2-dibromobenzene
Br
Br
1,3-dibromobenzene
Aromatic Compound Reactions
H
H
H
H
HH
Br
H
H
H
HH
+ HBr+ Br2FeBr3
catalyst
H
H
H
H
HH
CH2CH3H
H
H
HH
+ HCl+ CH3CH2ClAlCl3
catalyst
Substitution reaction
Polycyclic Aromatic Hydrocarbons
22.4 Hydrocarbon Derivatives
Hydrocarbons that have additional atoms or groups different than Carbon and hydrogen (functional group)
The common functional groups are….
They exhibit characteristic chemistry
Alcohols contain the hydroxyl functional group and have the general formula R-OH.
C6H12O6 (aq) 2CH3CH2OH (aq) + 2CO2 (g)enzyme
CH2 CH2 (g) + H2O (g) CH3CH2OH (g)H2SO4
Biological production of ethanol
Commercial production of ethanol
Metabolic oxidation of ethanol
CH3CH2OH CH3CHO + H2alcohol dehydrogenase
The systematic name is obtained from parent alkane by removing the final letter –e and adding –ol.
Aldehyde and KetonesThey contain carbonyl functional group.
R C H
O
• Aldehyde have the general formula
R C R’
O
• Ketone have the general formula
H C H
O
H C
O
CH3 C
O
CH3H3C___________ ___________ ___________
The systematic name of aldehyde is obtained from parent alkane by removing the final letter –e and adding –al, and for ketone also by removing the final letter –e and adding –one.
Carboxylic acids and Estersthey contain the carboxyl functional group.
The systematic name is obtained from parent alkane by removing the final letter –e and adding –oic.
CH3COOH + HOCH2CH3 CH3 C O CH2CH3 + H2O
O
ethyl acetate
The esters are formed, if carboxylic acid reacts with alcohol:
The systematic name is obtained from parent alkane by removing the final letter –oic and adding –oate of the acid, e.g., ethyl ethanoate.
AminesThey are organic bases with the general formula RNH2
CH3NH2 + H2O RNH3+ + OH-
CH3CH2NH2 + HCl CH3CH2NH3+Cl-
The common names are often used for simple amines, and the systematic name is obtained by using the name amino for each –NH2 group, e.g., 2-aminobutane
They are used for making dyes and their main reaction is acid-base:
A polymer is a high molar mass molecular compound made up of many repeating chemical units.
Naturally occurring polymers
•Proteins
•Nucleic acids
•Cellulose
•Rubber
Synthetic polymers
•Nylon
•Dacron
•Lucite
22.5 Polymers
The simple repeating unit of a polymer is the monomer.
Homopolymer is a polymer made up of only one type of monomer
( CF2 CF2 )n
Teflon
( CH2 CH2 )n
Polyethylene
( CH2 CH )n
Cl
PVC
R groups on same side of chain
Isotactic
R groups alternate from side to sideSyndiotactic
R groups disposed at random
Atactic
Stereoisomers of Polymers
22.2
Proteins
Amino acids are the basic structural units of proteins. An amino acid is a compound that contains at least one amino group (-NH2) and at least one carboxyl group (-COOH)
+H3N C C N C C O- + H2O
H
R1
H
R2
O O
H
+H3N C C O- + +H3N C C O-H
R1
H
R2
O O
Peptide bond
22.3
22.3
Protein Structure
22.3
Carbon
Nitrogen
Oxygen
R group
Hydrogen
The structure is held in position by intramolecularhydrogen bonds (………)
Protein Structure
22.3
Protein Structure
22.3
Intermolecular Forces in a Protein Molecule
ionic forces
ionic forces
hydrogenbonds dispersion
forces
dispersionforces
dispersionforces
dipole-dipoleforces
Hydrogen Bonds in Parallel and Antiparallel β-pleated Sheets
22.3
Protein Structure
22.3
The structural changes that occur when oxygen binds to the heme group in hemoglobin.
Nucleic Acids
Nucleic acids are high molar mass polymers that play an essential role in protein synthesis.
1. Deoxyribonucleic acid (DNA)
2. Ribonucleic acid (RNA)
DNA molecule has 2 helical strands. Each strand is made up of nucleotides.
22.4
The Components of the Nucleic Acids DNA and RNA
22.4
Base-Pair Formation by Adenine and Thymine and by Cytosine and Guanine
22.4
Chemistry In Action: DNA Fingerprinting
22.4