chapter 22. organic and biological...
TRANSCRIPT
Chapter 22. Organic and Biological Molecules
Substances - Organic substances
- Inorganic substabces
Produced by living systems
1828 Friedrich Wöhler NH4OCN H2N C NH2
O
Heat
Ammonium Cyanate
Urea
Organic chemistry : The study of carbon-containing compounds and their properties.
Alkanes: Saturated Hydrocarbons
Hydrocarbons: compounds composed of carbon and hydrogen
Saturated hydrocarbon: carbon-carbon bonds are all single - alkanes
Unsaturated hydrocarbon: contains carbon-carbon multiple bonds - alkenes and alkynes.
CH C C
H
H
HH
H
CH C C
H
H
HC
H
C
H
H
HH
H
Alkanes
methane ethane
propane butaneC
H
H H
H
H
C
HH
H
C
H
C
H
C
HH
H H
H
H
C
H
C
H
C
HH
H C
H
H
H
H
H
C
H
C
H
H
HH
H
All C atoms have sp3 hybrides.
C
H
C
H
C
HH
H H
H
Hn
H3C CH2 CH3n≡
methylene
Alkanes: Saturated Hydrocarbons
AlkanesC
H
C
H
C
HH
H H
H
Hn
H3C CH2 CH3n≡
methylene
CnH2n+2
Alkanes: Saturated Hydrocarbons
Isomerism of Alkanes
Alkanes with more than 3 carbons (from butane) exhibit structural isomerism.
C
C CC
H
H
H
HH H
H
H
H
H
Butane≡ ≡
≡
≡ ≡ ≡
CH3
CH2
CH2
CH3CH3 CH2 CH2 CH3
CH3
CH
CH3
CH3CH3
CH CH3CH3
normal butane (n-butane)
isobutane
Pentane CH3 CH2 CH2 CH2 CH3
CH3 C CH3
CH3
CH3
CH2 CH CH3
CH3
CH3normal pentane (n-pentane)
isopentane
neopentane
H C C C C H
H
H
H
H
H
H
H
H
Alkanes: Saturated Hydrocarbons
Nomenclatures
1. For alkanes beyond butane, add -ane to the
Greek root for the number of carbons.
pentane hexane
heptane
2. For a branched hydrocarbon, longest continuous
chain of carbon atoms determines the root name.
CH3 CH2 CH CH2 CH3
CH2
CH2
CH3
six carbons => hexane
3. When alkane groups (alkyl) appears as substituents:
drop the -ane and add -yl.
4. Positions of substituent groups are specified by
numbering the longest chain sequentially. Location
and name of substituent are followed by root alkane
name.
CH2 CH2 CH CH2 CH3
C2H5
CH3
125 36 4
652 41 3
3-ethylhexane
5. For more than one substituents,
list substituents alphabetically.
And the prefix di-, tri-, .. are used
for multiple, identical substituents.
CH2 CH2 CH CH2 CH3
C2H5
CH3
C2H5
3,3-diethylhexane
Alkanes: Saturated Hydrocarbons
Nomenclatures
Ex) Draw the structural isomers for the alkane C6H14 and give the systematic name for each one.
hexane
2-methylpentane
3-methylpentane
2,3-dimethylbutane
2,2-dimethylbutane
Ex) Determine the structures of
a. 4-ethyl-3,5-dimethylnonane
b.4-tert-butylheptane
Alkanes: Saturated Hydrocarbons
Reaction of Alkanes
Alkanes are saturated so that they are not much reactive. => lubricating materials, plastics
Substitution reaction
CH4 + Cl2 → CH3Cl + HCl
CH3Cl + Cl2 → CH2Cl2 + HCl
CH2Cl2 + Cl2 → CHCl3 + HCl
CHCl3 + Cl2 → CCl4 + HCl
Chloromethane
Dichloromethane
Trichloromethane
(chloroform)
Tetrachloromethane
(carbon tetrachloride)
hn
hn
hn
hn
Cl2 → Cl· + Cl·hn
Combustion reaction
2C4H10(g) + 13O2(g) → 8CO2(g) + 10H2O(g)
butane
propane
Dehydrogenation reaction
CH3CH3 → CH2=CH2 + H2
Cr2O3
500 oC
Alkanes: Saturated Hydrocarbons
Cyclic Alkanes
Carbon atoms can form rings containing only carbon-carbon single bonds
cyclopropane
60o 88o
cyclopropane cyclobutane
weak and strained : reactive
cyclopentane cyclohexane
tetrahedral angles: stablecyclohexane
more stable
12
5 3
6
4
1-isopropyl-3-methylcyclohexane 1-ethyl-2-propylcyclobutane13
4 2
substituents: alphabetical order
Alkenes and Alkynes
Alkenes: hydrocarbons that contain at least one carbon-carbon double bond.
H
C C
H
H
H
ethene ethane
1. Root hydrocarbon name ends in -ene
Nomenclatures
2. With more than 3 carbons, double bond is indicated by the lowest numbered carbon atom in the bond.
C C
CH3
H
H
H
propene
C C
H
H
CH2
H
CH3
1-butene cis-2-butene trans-2-butene
Alkenes and Alkynes
Alkynes: hydrocarbons that contain at least one carbon-carbon triple bond.
C C HH
ethyne
(acetylene)
1. Root hydrocarbon name ends in -yne
Nomenclatures
2. With more than 3 carbons, triple bond is indicated by the lowest numbered carbon atom in the bond.
HC C CH3 HC C CH2 CH3 H3C C C CH3
propyne 1-butyne 2-butyne
CH3
CH CH
CH3
CHC2H5
CH3
C C CH
CH2 CH3
CH2 CH3
CH2
CH3
cyclohexene 4-methylecyclopentene 4-methyl-trans-2-hexene 5-ethyl-3-heptyne
Alkenes and Alkynes
Reactions of Alkenes and Alkynes
Unsaturated hydrocarbons => addition reaction in which (weaker) p bonds are broken and
new (stronger) s bonds are formed to atoms being added
Hydrogenation reaction
CH2=CHCH3 + H2 → CH3CH2CH3
Catalyst/Pt, Pd, Ni
1. Adsorption and activation of the reactants.
2. Migration of the adsorbed reactants on the surface.
3. Reaction of the adsorbed substances.
4. Escape, or desorption, of the products.
Step for heterogeneous catalysis weakening the H-H bond,
or reducing the activation
energy
Halogenation reaction
CH2=CHCH2CH2CH3 + Br2 → CH2BrCHBrCH2CH2CH3
Chapter 12.
Polymerization
Aromatic Hydrocarbons
Aromatic hydrocarbons: a special class of cyclic unsaturated hydrocarbons.
Benzene (C6H6)
Reactions: No addition reaction but substitution reaction
+ Cl2 →
Cl
+ HCl
+ HNO3 →
+ CH3Cl →
NO2
CH3
+ H2O
+ HCl
Chlorobenzene
Nitrobenzene
Toluene
Aromatic HydrocarbonsNomemclatures
12
5 3
6
4
1,2-dichlorobenzene
Cl
Cl
Cl
Cl
o = ortho
m = meta
p = parao
m m
o
p
o-dichlorobenzene
Hydrocarbon DerivativesHydrocarbon derivatives : Hydrocarbons having additional atoms or groups of atoms,
called functional groups.
Hydrocarbon DerivativesAlcohols
Functional group : -OH R C
H
H
OH C
R
R'
H
OH C
R
R'
R"
OH
primary alcohol secondary alcohol tertiary alcohol
Nomenclature : -ol
CO + 2H2 → CH3OH
400oC
ZnO/Cr2O3
(methanol : wood alcohol, starting material for higher order organic compounds)
C6H12O6 → 2CH3CH2OH + 2CO2
yeast
glucose ethanol
Hydrocarbon DerivativesAlcohols
C6H12O6 → 2CH3CH2OH + 2CO2
yeast
glucose
CH2=CH2 + H2O → CH3CH2OH
catalyst
1,2-ethanediol (ethylene glycol)
HO-CH2-CH2-OH
Polyhydroxyl (poly-ol)
Aromatic alcohol
OH
phenol
OH
Ex) name and primary, secondary, tertiary ?
OH
Br
Cl OH
2-butanol (seconary alcohol)
6-bromo-2-methyl-2-hexanol (tertiary)
3-chloro-1-propanol (primary)
Hydrocarbon DerivativesAldehydes and Ketons
Synthesis : oxidation of alcohol
OH
ox
H
O
primary aldehyde
ox
OOH
secondary ketone
CH
O
O
CH3
OH
CH CH
CH
O
Vanillin
Cinnamaldehyde
Functional group :
Nomenclature : -al -one
R
C
H
O
R
C
R'
OCarbonyl group
pleasant or unpleasant odor
(aldehyde)
Hydrocarbon DerivativesCarboxylic Acids and Esters
Functional group :
Nomenclature : -ic acid -ate
Carboxyl group
R
C
O
OH R
C
O
O
R'
Synthesis of carboxylic acids :
oxidation of primary alcohol with
strong oxidant
OH
O
OH
KMnO4(aq)
Synthesis of esters : carboxylic acid + alcohol
O
OH H O O
O
ethyl acetate
+ H2O
O
OH
OHOH
O
+ H2O
O
OH
O
O
salicylic acid aspirin
O
O
n-amyl acetate (n-pentyl acetate)
O
O
n-octyl acetate
sweet odor
(ester)
Hydrocarbon DerivativesAmines
Functional group : -NR2 (R=H, R, R')
R C
H
H
OH C
R
R'
H
OH C
R
R'
R"
OH
primary alcohol secondary alcohol tertiary alcohol
Nomenclature : amine.
For complex molecules amino
as a substituent
NH2
2-aminobutane
Bad "really bad" odor (amine)
F F
PolymersPolymers: large, usually chainlike molecules that are built from small molecules called monomers.
polyester
nylon
N CH2 N C
H H O
CH2 C
O
n6 4
Natural Polymers
The Characteristics of living Organisms
• Structurally complicated and highly organized -Intricate internal structure
• Extract, transform, and use energy from their environments
• The capacity for precise self replication and self assembly
Molecular logic of life
• Diverse living organisms share common chemical features.
• The same basic structural units (cells)
• The same kinds of macromolecules (DNA, RNA, proteins)
• Made up of the same kinds of monomeric subunits (nucleotides, amino acids)
Nucleaic Acids
Natural Polymers
Carbohydrates
Proteins
The players of life
The playground
Natural PolymersProteins: Natural polymers made up of a-amino acids (molecular weight from 6000 to >1,000,000 g/mol
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
H
N
H
C
H
R OH
O
a-carbon
side chain
Amino acids
carboxyl groupamino group
H
N
H
C
H
R OH
O H
N
H
C
H
R' OH
O
H2N C
H
R
C
O
N
H
C
R'
H
COOH
+ H2O
dipeptide
peptide linkage
polypeptide
protein
Natural Polymers
Amino acidsProteins
a-helix
Natural PolymersProteins
1 2 3 4 5 6
H2N COOHLevels of protein structures
Primary: Sequence of amino acids in the protein chain.
C O H N
Secondary: Highly regular sub-structures- a-helix and strands of b-sheet. Secondary structures are locally defined,
meaning that there can be many different secondary motifs present in one single protein molecule (hydrogen
bonding determines this).
b-turnrandom-coil arrangement
b-sheet
Natural PolymersProteins
Levels of protein structures
Tertiary: The overall shape of the protein (determined by hydrogen-bonding, dipole-dipole interactions,
ionic bonds, covalent bonds and London forces).
ionic hydrogen covalent London dipole-dipole
Quaternary structure: complex of several protein molecules or
polypeptide chains, usually called protein subunits in this context, which
function as part of the larger assembly or protein complex.
Natural PolymersProteins
The tremendous flexibility in the various levels of protein structure alls the tailoring of proteins for a wide
range of specific functions. Proteins are the "work-horse" molecules of living orgams.
Denaturation: Breaking-down of three dimensional structure of a protein
Heat
UV
X-ray
Nuclear radio acivity
Natural PolymersCarbohydrates
Food source for most organisms and structural material for plants
Empirical formula = CH2O
containing the functional groups of ketone at 2 position (or aldehyde at 1 position) and alcohols
Monosaccharides (simple sugars) :
Triose (3 carbons), Tetrose (4 carbons), Pentose (5 carbons), Hexose (6 carbons).......
enantiomers
chiral center
CHO
C OHH
C OHH
C OHH
CH2OH
CHO
C OHH
C OHH
C OHH
CH2OH
three chiral carbons => 8 optical isomers
CH2OH
C O
C OHH
C OHH
CH2OH
C
C OH
C OHH
C OHH
CH2OH
O
H
H
aldopentoseketopentose
CHO
C OHH
C OHH
C OHH
CH2OH
Ex) How many chiral carbon in the following aldopentose?
ketopentose => two chiral catbons => 4 optical isomers
pentose => two structural isomers (aldo and keto) => 12 optical isomers
Cyclization of D-fructose
Cyclization of D-glucose →
Natural PolymersCarbohydrates
C5H10O5
C6H12O6
Cyclization of Monosaccharides: monosaccharides
usually form a ring structure in aqueous soultion
Natural PolymersCarbohydrates
Dimerization of Monosaccharides: disaccharides
+H2O
-H2O
Polymerization of Monosaccharides: polyisaccharides
a-D-Glucose
=>
b-D-Glucose
=>
Starch
Cellulose
amylose (chain)
amylopectin
(branch)
Natural PolymersNucleic Acids
DNA (deoxyribonucleic acid): 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)
Monomeric unit of nucleic acids: nucleotides
3. Phosporic acids (H3PO4)
2. N-containing Organic bases
Ribose (a pentose)
1. Deoxyribose for DNA and ribose for RNA
Polymerization of Nucleotides
Forming of Nucleotides
nucleoside
nucleotide
Nucleic Acids
CH2
CH2
Base
O
HO
HH
HH
O
PO
OH
OH
Base
O
HOH
HH
HH
O
PO
OH
OH
H
Dimerization of Nucleotides
H2O
Base
O
HO
HH
H
CH2
H
O
PO
OH
OH
Base
O
HOH
HH
H
CH2
H
O
PO OH
Natural Polymers
Natural PolymersNucleic Acids
Structure of DNA: Double-helical structure with complimentary based on the two strands
Cell division and transmission of genetic information
Natural PolymersNucleic Acids
Synthesis of proteins
mRNA (messenger RNA)
rRNA (ribosomal RNA)
Ribosome = complex of rRNA and proteins
Gene : A part of DNA which will be
expressed into a protein.
Natural PolymersNucleic Acids
Synthesis of proteinstRNA (transfer RNA)
김성호
1970's
Natural PolymersNucleic Acids
Synthesis of proteins2006 Nobel Prize in Chemistry
Roger Kornberg (2006)Arthur Kornberg (1959)
ChemistryPhysiology and Medicine
Why do we have to study Chemistry?
Chemical Bonding
Diversity in the Universe
creates
Chemical Bonding
Why do we have to study Chemistry?
We
Diversity in the Universe
understand
Why do we have to study Chemistry?
We
Diversity in the Universe
create
Why do we have to study Chemistry?
For Better Life
Good Luck for Your Finals !