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Organic
Chemistry
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1
Organic chemistry is the study of carbon-containing
compounds.
Common Elements in
Organic Compounds
Lack of metals (cations) indicates all covalent bonding
SciShow: IDTIMWYTIM “Organic”
www.youtube.com/watch?v=9j2a0q14wOs
Review: Covalent Bonding
Atoms will normally have a number of bonds equal to the
number of valence electrons needed.
Bonds Formed
4A: 4 x C single bonds
4
3
2
1
1 x C double and 2 single bonds
1 x C triple and 1 single bond
2 x double bonds
5A: 3 x N single bonds
1 x N double and 1 single bond
1 x N triple bond
:
:
6A: 2 x O single bonds; 1 x O double bond
7A: 1 x F single bond
Friedrich Wöhler accidentally
synthesized urea in 1828
“When ammonium cyanate is heated, it produces urea
without benefit of a kidney, a bladder, or a dog.”
• Used biologically for excess nitrogen excretion
• First time a biomolecule had been synthetically created
• Was believed organics could only be made by living things
• Opened gateway to applying chemistry to biological systems
Classification of Hydrocarbons
Hydrocarbons are made up of mostly hydrogen and carbon.
(Contains rings
with resonance)
Why is Carbon special? Versatility and Stability
1. Versatile bonding: single, double, triple.
2. Forms stable bonds with other Carbon atoms.
3. Forms stable bonds with other non-metal elements.
The CAS (Chemical Abstracts Service) Registry contains
more than 95 million unique chemical substances on file.
Over 80% of them are Organic substances (Carbon compounds).
• Small compounds (Acetone, ibuprofen, octane, Vitamin A, ATP)
• Biomolecules (Proteins, DNA, Carbohydrates, Lipids) → oil/gas
• Plastics (Rubber, PVC, Teflon, Vinyl, Propylene, Styrofoam)
Why so many?
Carbon is versatile
4 x single bonds
Carbon forms stable bonds
• Smaller atomic size than Silicon
1 x double and 2 single bonds • Shorter bonds = Stronger bonds
2 x double bonds
1 x triple and 1 single bond
• Can bond with a variety of atoms
The Petroleum Industry
Crude Oil: Complex mixture of 100’s
of hydrocarbon variants
→“Cracking”: Separate
mixture out by boiling point
C1-C4
C6-C12
C5-C12
O2
C11-C16
C14-C18
C15-C24
Alkanes – simplest hydrocarbon
Alkanes only single covalent bonds
• Have the general formula CnH2n+2
where n = 1,2,3,…
• Said to be “saturated” because they contain the maximum
number of hydrogen atoms that can bond with the number of
carbon atoms in the molecule
CH4
C2H6
C3H8
methane
ethane
propane
8
both
C4H10
Structural isomers are molecules that have the same
molecular formula but different structures.
Example 24.1
How many structural isomers can be identified for pentane,
C5H12?
H
H
H
H
H
H
C
C
C
C
C
H
H
H
H
H
H
n-pentane
(b.p. 36.1 oC)
The lack of branching in npentane allows for closer interaction
between molecules and stronger
intermolecular forces.
Physical Properties of Some Alkanes
• All alkanes end with “-ane”
• Prefix determined by the number of carbon atoms
• As mass is added, Melting/Boiling point go up
-C1 to C3 are gaseous at room temperature
-C4 to C8 are highly volatile liquids
11
Organic Structure Representation
• Octonol: C8H18O or
C8H17OH
• CH3CH2CH2CH2CH2CH2CH2CH2OH
• CH3(CH2)7OH
• Skeletal
Hydrogens are omitted in drawing hydrocarbons and left to be understood
(knowing Carbon needs 4 bonds); Non-carbon atoms are explicitly shown
• Space-filled
Organic Representation
Alkane Nomenclature
1. The parent name of the hydrocarbon is that given to the longest
continuous chain of carbon atoms in the molecule.
CH3
CH3
1
CH2
2
CH2
3
CH
4
4-methylheptane
CH2
5
CH2
6
CH3 heptane
7
2. An alkane less one hydrogen atom
is an alkyl group.
CH4
methane
CH3
methyl
14
Alkane Nomenclature
3. Number in the direction that gives the smaller numbers for the
locations of the branches.
CH3
CH3
CH3
1
CH
2
CH2
3
CH2
4
CH3
5
CH3
CH2
1
2
CH2
3
CH
4
4-methylpentane
1
C
2
CH3
3
CH3
2-methylpentane
CH3
CH3
2-methylpentane
CH3
5
Alkane Nomenclature
4. Use prefixes di-, tri-, tetra-, when there is more than one alkyl
branch of the same kind.
CH3
1
CH3
CH3
CH
CH
2
3
CH2
4
CH2
5
CH3
6
2,3-dimethylhexane
CH3
CH3
1
CH2
2
C
3
CH2
4
CH2
5
CH3
6
CH3
3,3-dimethylhexane
16
Alkane Nomenclature
5. Use previous rules for other types of substituents.
CH3
1
Br
NO2
CH
CH
2
3
CH3
4
2-bromo-3-nitrobutane
Cl
CH2
1
F
CH2
2
CH
3
CH3
4
1-chloro-3-fluorobutane
17
Example Naming Hydrocarbons (nomenclature)
Give the IUPAC name of the following compound:
The compound is 2,2,4-trimethylhexane.
18
Example Drawing Hydrocarbons from nomenclature
Draw the structure of 3-ethyl-2,2-dimethylpentane.
Draw the structure of 2-amino-4-isopropyl-5-propyl-octane.
19
Alkane Reactions
Combustion
CH4 (g) + 2O2 (g)
CO2 (g) + 2H2O (l)
DH0 = -890.4 kJ/mol
Methane (Natural gas)
2C2H6 (g) + 7O2 (g)
4CO2 (g) + 6H2O (l)
DH0 = -3119 kJ/mol
The greater the number bonds, the greater energy stored.
Halogenation
CH4 (g) + Cl2 (g)
Cl2 + energy
light
CH3Cl (g) + HCl (g)
Cl• + Cl•
(Can form radicals – atoms with unpaired e-)
Very reactive
Hydrocarbon Power! - Crash Course Chemistry #40
www.youtube.com/watch?v=UloIw7dhnlQ
Chirality: isomers with identical bonding,
but different spatial arrangement.
• Enantiomers – non-superimposable isomers with
identical mirror images (S & R types).
• They appear identical, but are chemically distinct.
• Chiral compounds were known to be optically active
because they could rotate plane polarized light.
• 19 of the 20 amino acids are chiral (L-form)
TedEd: What is Chirality?; www.youtube.com/watch?v=71GjsRnsoL8
Optical Isomerism (stereoisomers)
No chiral center
with 3 unique
bonds on C
Carbon is a chiral
center with 4
unique bonds
achiral
chiral
Alice's Adventures in
Wonderland (1865)
by Lewis Carroll
23
(S) and (R) Thalidomide Isomers
•Introduced in the 1950’s as a “wonder drug” for morning sickness
• Resulted in 10,000’s of birth defects
• (R) form is effective, but the (S) form can bind to DNA to
produce mutagenetic effects.
• Many organic reactions produce a racemic mixture of equal
parts.
Example Chirality
Which of the following molecules are chiral? Circle the chiral centers.
Chiral
Glycine; Achiral
Chiral
Ibuprofen; Chiral
Sold as a racemic mixture
Alkenes (unsaturated)
Alkenes have the general formula CnH2n where n = 2,3,…
• Contain at least one carbon-carbon double bond
• Name ends with –ene (or -diene, -triene)
CH2
CH CH2
1-butene
CH3
CH CH CH2
1,3-butadiene
CH2
Geometric Isomers:
Diastereomers
Cis: Larger R’s
on same side
Cl
Cl
C
H
Cl
C
C
H
cis-dichloroethylene
H
Trans: Larger R’s
on opposite side
H
C
Cl
trans-dichloroethylene
Cis-isomers
Trans-isomers
Geometric Isomers:
Diastereomers
cis-1,2-dichloroethene
trans-1,2-dichloroethene
cis-butenedioic acid
(maleic acid)
trans-butenedioic acid
(fumaric acid)
Oleic acid (~70% olive oil)
Elaidic acid
*Trans-fats are
considered worse
nutritionally because
they pack tightly
(more difficult to
break apart as they
stick together)
Less branching leads to stronger London Dispersion forces
(e.g. higher melting point)
Cis-Trans Isomerization in the Vision Process
Electron micrograph
of retinal rods
28
Example
Give the IUPAC name of the following Alkenes:
• Counting carbons starts at 1st double bond (not 1st substituent)
NH2
Br
C
H
1
C
CH2
CH3
4
H2C
CH
CH2
CH2
CH2
H
1-bromo-cis-1-butene
3-amino-1,4-pentadiene
Neither cis or trans
29
Alkene Reactions
Cracking (breaking down to smaller hydrocarbons)
C2H6 (g)
Pt
catalyst
CH2
CH2 (g) + H2 (g)
Addition Reactions
CH2
CH2 (g) + HBr (g)
(Oxidation: lose H’s)
CH3
CH2Br (g)
(Reduction: gain H’s)
CH2
CH2 (g) + Br2 (g)
CH2Br
CH2Br (g)
d+ d-
and/or
Markovnikov’s rule: When adding polar reagents to alkenes, the
positive portion (d+) of the reagent (usually hydrogen) adds to the
carbon atom that already has the most hydrogen atoms.
31
Alkynes (Triple bonds)
Alkynes have the general formula CnH2n-2 where n = 2,3,4,…
• Contain at least one carbon-carbon triple bond
• Name ends with –yne
CH
C
CH2
CH3
CH3
1-butyne
C
C
CH3
2-butyne
(very rare in biochemistry)
Production of acetylene
CaC2 (s) + 2H2O (l)
C2H2 (g) + Ca(OH)2 (aq)
Crash Course: Alkenes & Alkynes
www.youtube.com/watch?v=CEH3O6l1pbw
32
Cycloalkanes
Alkanes with carbon atoms joined in rings.
• They have the general formula CnH2n
• Each ring adds a degree of unsaturation (2 less H per ring)
• Begin with the prefix Cyclo-
33
H
H
H
C
C
C
C
C
C
Aromatic Hydrocarbons
H
H
C
H
H
benzene
C
C
C
C
H
H
H
Phenol
H
C
H
TNT
Aspirin
Electron micrograph
of benzene
Benzene compounds were originally coined Aromatic due
to being commonly volatile with distinct odors (aroma).
While aromatic may often have smells, there is no firm rule
stating one must trigger an olfactory response.
Strawberry
Vanillin
Naphthalene
(moth balls)
Eugenol (Carnations)
Guaiacol
(roasted coffee)
(Bacon)
Aromatic rings have resonance (delocalized
electrons) across their p-bonds: increases stability
• Benzene (benzyl) when main component
• Phenyl group when a substituent
Nitrobenzene
3 of the 20 amino acids
possess aromatic groups
trans-2-phenyl-2-butene
Crash Course: Aromatic Compounds
www.youtube.com/watch?v=kXFEex-dABU
Chemistry In Action: Ice That Burns
methane hydrate
~1013 tons of carbon content
Found on ocean sea-bed
Difficult to harness energy
37
Functional Groups
Specific groups of atoms or bonds within molecules that
are responsible for the molecules’ characteristic properties
Functional Group Chemistry
Alcohols contain the hydroxyl functional group (R−OH).
• Form Hydrogen bonds
• Not Acidic; does not deprotonate
• 3 of the 20 amino acids possess –OH
• Nomenclature suffix: –nol
Drinking Alcohol
Rubbing Alcohol
Wood
Alcohol
“AntiFreeze”
BPA
←
Oxalic Acid - Kidney
Ethanol Production and Metabolism
Biological production of ethanol
Enzymes
C6H12O6 (aq)
Sugar
2CH3CH2OH (aq) + 2CO2 (g)
“Fermentation”
Commercial production of ethanol
CH2
CH2 (g) + H2O (g)
H2SO4
Metabolism of ethanol
CH3CH2OH
CH3CH2OH (g)
Acetaldehyde
alcohol dehydrogenase
CH3CHO + H2
“Hangover molecule”
Acetylaldehyde dehydrogenase enzyme
O
Disulfiram inhibitor
“Antabuse”
H
C CH3
Acetaldehyde
O
H C OH + H2
Acetic Acid
Functional Group Chemistry
Ethers have the general formula R−O−R′.
Diethyl ether: solvent
Lignin: found in cell wall of plants
Polysaccharides: etherlinkage between sugars
Polyethylene glycol:
Common polymer in pharmaceuticals,
cosmetics, and commercial use.
crown ether
Functional Group Chemistry
Aldehydes and Ketones contain the Carbonyl group.
O
• Aldehydes have the general formula
R C H
• Nomenclature suffix: -al
O
H
C H
Formaldehyde
Cinnamaldehyde
(2E)-3-phenylprop-2-enal
(Methanal; Embalming
Fluid)
O
H
CH3
C CH3
Acetyl
Acetaldehyde
(Ethanal)
O
• Ketones have the general formula
R C R′
• Nomenclature suffix: -one
Fructose
O
H3C C CH3
acetone
Acetophenone
(1-phenylethanone)
(2-propanone,
Nail polish remover)
Functional Group Chemistry
Carboxylic acids contain the carboxyl ( −COOH ) group.
• A Carboxyl group is a carbonyl next to a hydroxyl group
• All amino acids have a carboxylic acid used in peptide linking.
• Have low pKa and deprotonate easily.
• Nomenclature suffix: –ic acid
Fatty acids
CH3(CH2)nCOOH
Esters have the general formula R′COOR
Ester-linkages in lipids
• Formed from reaction of alcohol
& carboxylic acid
• More easily broken than ethers
• Nomenclature suffix: -oate
Esters have characteristic fruity aromas
Strawberry
Oranges
Benzyl acetate
Octyl acetate
Grapes
Methyl anthranilate
Apples
Bananas
Pentyl pentanoate
Pentyl acetate
Functional Group Chemistry
Amines are organic bases with the general formula R3N.
• R-NH2 + H+ → R-NH3+ (can be neutral or positively charged)
• All amino acids have an amine at their base
Primary amine
Secondary amine
Tertiary amine
+NH
3
Glutamine
Porphyrin ring: region in
Hemoglobin bound to Fe+2 used to
bind O2 (both 2° and 3° amines)
Functional Group Chemistry
Amides possess a carbonyl adjacent to an amine.
• NOT Basic; does NOT accept H+ to become + charged
• Very stable bond due to resonance
+NH
3
Glutamine
Amines react with Carboxylic acids to form Amide bonds
• Called a peptide bond in proteins when linking amino acids
Functional Group Chemistry
Thiols possess Sulfur atoms
•Similar bonding as oxygen, but weaker bonds
•Notable odor resembling garlic or rotten eggs
Vitamin B1: Thiamine
Thioacetone
S
C
H3C
CH3
SciShow: 5 of the World's Most Dangerous Chemicals
www.youtube.com/watch?v=ckSoDW2-wrc
Disulfide Bridges
Spot the Functional Groups in the molecules
Acetoacetic acid
Cinnamaldehyde
Heme A
Maltose
Amine (amino)
Amide
Alcohol (hydroxyl)
Aldehyde
Aromatic (Phenyl)
Ester
Ether
Carboxylic Acid
(Carboxyl)
Ketone (Carbonyl)
Thiol
Spot the Nine Functional Groups in the molecule: C18H12N2O9
(2Z)-5-[5-(acetyloxy)-3-(2-amino-2-oxoethyl)-2-hydroxyphenyl]-4-amino-5-oxo-2-[(2-oxoethoxy)methyl]pentanoic acid
Crash Course: Functional Groups; www.youtube.com/watch?v=hlXc_eEtBHA
Crash Course: Organic Nomenclature; www.youtube.com/watch?v=U7wavimfNFE
Other Notable groups
Steroids:
Purines:
Pyrimidines:
Testosterone
Adenine
Cytosine
Cholesterol
Caffeine
Barbiturates
Reactions: The Science of Caffeine
www.youtube.com/watch?v=YuJOhpNS0IY
Ribose:
Found in
DNA/RNA
ATP
*NADH
Organic Reactions
• Heterolytic – polar reactions
– More common reaction in biological reactions
– Bonding e- pair go with 1 atom
:
• Homolytic – radical reactions
– Less specific
– Forms free radicals by atoms splitting the e- pair
Heterolytic (Polar) Reactions
• Occur between attraction of partial + & – charges on
different functional group atoms in molecules
• Electron-rich atom react with electron-poor atoms.
– Nucleophile – electron rich (lone pair; d-) and “nucleusloving”. Donate electron pair to form bond.
– Electrophile – electron poor (d+) and “electron-loving”.
Polarity/Stability
The more polarized a bond is the more prone it is to react.
d-
d+
d+
d+
d-
d• Added Carbonyl increases C─O bond polarity.
• C─O bond is more easily broken in esters over ethers.
Condensation and Hydrolysis reactions
+ H2O
Alcohol
Acid
Acid
Ester
2 Alcohols to ether
Amine
Amide
Homolytic (Radical) Reactions
Initiator: Cl2 + UV light → 2Cl•
Ethylene
Will continue to add ethylene units until it ethylene runs out and reacts
with another radical to cease radical reaction.
repeating unit (monomer); n can equal 100’s to 100,000’s
Polyethylene
Plastic
A polymer is a large compound made up of many
repeating chemical units. (poly = many; mer = unit)
Natural polymers
Synthetic polymers (plastics)
• Proteins – Amino acid
• Polyethylene
• DNA – Nucleic acid base
•Polypropylene
• Cellulose - Carbohydrates
• Polyvinlylchloride (PVC)
• Rubber - Isoprene
• Nylon
• Teflon
• Kevlar
Proteins bound to DNA
Teflon: polytetrafluoroethylene
Changing the monomer composition changes the
properties and type of plastic.
Polypropylene
Propylene
Polyvinyl
chloride
(PVC)
Chloro-ethylene
Polystyrene
(Styrofoam)
Polytetrafluoroethylene
(Teflon)
Copolymers possess
more than one
type of monomer
Acrylonitrile butadiene rubber
Styrene-butadiene rubber
Crash Course: Polymers
www.youtube.com/watch?v=rHxxLYzJ8Sw
http://www.compoundchem.com/2014/06/22/kevlar/
Chemical Identification: IR Spectroscopy
Covalent bonds have various motions that have infrared frequencies
C=C
Bond Bending
61
Chemical Identification: 13C NMR
13C
nuclei align in a magnetic field; a pulse of a precise frequency can
cause them to flip alignment; dependent on local chemistry
Alcohol
C13-O-H
Vanillin
Ether
C13-O-C13
Aromatic;
C=C
Aldehyde
(13C=O)H
Chemical Identification: 1H NMR
Much like 13C NMR, 1H orients in a magnetic field and is flipped by
a specific frequency that is dependent on local chemistry.
Ether
1H-C-O-C
Vanillin
Aromatic; Alcohol
C-O-1H
C=C
Aldehyde
(C=O)1H