Module 1: Organic Chemistry
Organic Chemistry Bond type
Organic compounds o Single “an”
Contains carbon o Double “en”
Except CO2, CO3-2 o Triple bond “yn”
Classify according to functional group Prefixes
Family/class o 1 meth
Similar structure and o 2 eth
reactivity o 3 prop
Ex. CH3OH(methanol), o 4 but
CH3CH2OH(ethanol) o 5 pent
“-ol” – hydroxyl functional Suffix & Prefix
group o Substituents
o Suffix
Hydrocarbons (C & H) Highest priority substituent
only
CARBONYL RCOOH
C–C ALKANES C=O
GROUP RCOOH derivatives
RCHO
C=C AKENES RCOH
ALDEHYDES RCOR
(CHO – Formyl) ROH
CARBOXYLIC RSH
RCOO RNH2
C C ALKYNES ACIDS (COOH –
H C C
Carboxyl)
C=C
AROMATIC C–C
CARBOXYLIC
CMPDS / RX,ROR,RSR –
DERIVATIVES
ARENES never suffix
Ex. CH3CH2Cl
ALKYL Ethyl chloride
RX RCOOR ESTERS Chloroethane
HALIDES
CH3CH2OCH3CH2
RNH2 AMINES RCONH2 AMIDES Ethyl ether
ROR ETHERS CONH2 CARBAMOYL Ethoxyethane
THIOETHE Practice Set 1
RS (super RCOOC 1. Pentane: 3-methylpentane
RSR ANHYDRIDES
analog of OR
ethers)
ROH ALCOHOLS RCOX ACYL HALIDE
2. Rule: alphabetization
THIOLS
3-ethyl-4-methylhexane
RSH (sulfhydryl/ RCO ACYL
mercapto)
RC= ACETYL
KETONES CH3CO
OR (simplest acyl)
3. 2-aminopropan-1-ol (1-propanol)
NOMENCLATURE
Organic compounds may have different
names 4. 1-chlorobut-2-en-2-ol
Ex. CH3COOH – acetic acid(semi-
systematic)/ethanoic acid(systematic)/(dil.)
vinegar(trivial)
5. for multiple subs, add multiplier prefix
IUPAC (International Uni…)
1,1,2-trimethylcyclohexane
Formulated the rules on nomenclature
Format:
Prefix-parent-bond type-suffix
Parent
o Most important
o Usually the longest chain
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6. Naming esters: (alkyl-alkanoate) o Heterocyclic
Pyrole
Pyran
Thiophene
With hetero atom
a. Methyl propanoate Purine
(nitrogenous base)
Oxazone (with O & N)
b. Ethyl ethanoate/ethyl acetate Aromatic
Aliphatic – not aromatic
Cumulated – system of double bond
(no single bond between the double bonds)
7. Parent contains the most number of
substituents
a. 2-amino-1-phenylpropan-1-ol
(phenylpropanolamine)
Isolated - system of double bond
(>1 single bond between the bonds)
8. N – locant (not attached to the parent) Conjugated - system of double bond
a. 4-[(N-acetyl)amino]phenol / (alternating double-single bonds)
para-[(N-acetyl)amino]phenol / ex. Benzene
Paracetamol
Saturated – filled up with H’s
Unsaturated – not filled up with H’s
o Ex. CH3CH2CH3 – propane
(saturated)
Formula: CnH2n+2
Every additional bond
TERMINOLOGY reduces
Acyclic 2 Hydrogens
o “A”cyclic – not cyclic Alkenes: CnH2n
o Linear/straight chain (unsaturated)
o Branched Alkynes: CnHn+1
(unsaturated)
Cyclic o Cyclopropane – C3H6
o Carbocyclic – all are carbon Def 2 H
Benzene Every ring closure reduces 2
Cyclohexane H
Naphthalene (bicyclic Reasons of H loss
compound) Double or triple bond
Anthracene (tricyclic) Ring closure
Has a 2C bridge
BONDING AND HYBRIDIZATION
Spiro – 1 C (spiroatom) A. Generalities
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B. Bonding of Carbon STRUCTURAL EFFECTS
Affect the stability of a compound(may inc
or dec stability)
Stable = neutral = unreactive
Unstable = charged = reactive
1. Inductive effect
Influence based on the stability of a
SIGMA PI compound based on its
electronegativity (or lack of)
s orbital p orbital Ex.
Head-on collision Sideways overlap
Classifications based on a-carbon
Strong Weaker
First Anything after
Single: sigma: strong
Double: 1 1: stronger
Triple: 1 2: strongest
C. Hybridization
Inductive Effect and acidity
o Acidity
Ability to release H+
ions
More reactive, more
acid
Rank the ff by acidity
Practice Set 2
a.
b.
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Rank by stability b. Angle strain
For halogens, larger sizes means For cyclic compounds
greater instability Deviation from the original
High size = high reactive/unstable 109.5o/tetrahedral shape of
HI>HBr>HCl>HF sp3 carbons
Cyclohexane – almost no
angle strain; most stable
cyclic
2. Resonance / Pi electron delocalization
sp2 atoms in conjugated systems
Delocalization – continuously
moving
Ex.
Resonance/
Canonical
structure c. Torsional strain
Steric effect due to rotation of
single bonds
Benzene – Stability:
inc stability Staggered > Eclipsed
Anti > Gauche > Syn
Ex. Ethane
Carbonate
3. Strains
Structural effects that decrease
stability of a compounds
a. Steric effects/steric hindrance
Competition for space due to
bulky groups
STAGGERED ECLIPESED
Ex. (MORE STABLE) (LESS STABLE)
Cl
STAGGERED ECLIPSED STAGGERED ECLIPSED
ANTI GAUCHE GAUCHE SYN
(MOST STABLE) (LEAST STABLE)
ISOMERS
Compounds with same molecular formula
but different structure
CHAIN/SKELETAL
ISOMER
CONSTITUTIONAL POSITIONAL
FUNCTIONAL
CONFORMATIONAL
SPATIAL/
STEREOISOMERS
CONFIGURATIONAL
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a. Constitutional Structure ii. Optical
Not same connectivity
Optical activity
1. Chain/Skeletal Ability to rotate plane-polarized light
Different branching S – counterclockwise
R – clockwise
2. Positional
Difference in position/locant
ex. Propan-1-ol (1-propanol)
Propan-2-ol (Isopropyl alcohol) (S) (R)
3. Functional
Difference in functional group
Chirality
b. Spatial/Stereoisoemer Possesses a chiral carbon – contains 4
1. Conformational Isomer different substituents
Relative arrangements of the
bonds of a single compound in Enantiomers/Mirror image
space o Nonsuperiosable
ex. Diasteriomer
Cyclobutane o Not enantiomer
o Opticaly active
“Butterfly” Mesocompounds
o Chiral but optically inactive
Clyclopentane
“Envelope”
2. Configurational Isomer
i. Geometric
Due to restricted motion
of bonds
Cis-Trans
Applicable for di-substitution
INTRODUCTION TO ORGANIC REACTION MECHANISM
1. A + B = AB – addition
2. AB = A + B – elimination
3. AB + CD = AC + CD – substitution
Attacking groups (depends on type of cleavage)
E/Z system 1. Hemolytic cleavage
Tri/tetra-substitution A-B = A. + B. (Free radicals) R.
Follows cahn-ingold-prelog (CIP) A-B = A- (Nu- nucleophile) + B+ (E+
rules for prioritization electrophile)
High atomic number high priority Ex.
i. SN – nucleophile substitution
ii. AE – electrophile addition
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ALKANES
“PARRAFINS”
HC’s with all single bonds (saturated)
Very stable/unreactive
Ex. Ethane
Reactivity
1. Combustion
For organic
compounds(hydrocarbons)
Use of heat and oxygen
a. Complete
CXHX = CO2 + H2O
B. Reaction of benzene mechanism (SE)
b. Incomplete
Insufficient/limited supply of
oxygen
CXHX = CO2 + CO + C(soot) +
H2O
2. Cracking 1. Halogenation SE
Use of heat to break a HC into
smaller fragments
Used in the fuel industry
3. Halogenation (SR – free radical substitution)
Requires assistance from
U(sunlight) 2. Nitration
X2 = 2X. (Initiation phase)
Ex. Chain reaction
PROPAGATION
Phase
3. Sulfonation
4. Friedel-Crafts Alkylation
AROMATIC COMPOUNDS
A. Aromaticity
Criteria
1. Cyclic
2. All ring atoms must be sp2
Note: charged atoms are also
sp2
3. n = whole number in formula for
Hückle’s rule 5. Friedel-Crafts Acylation
4n + 2 = pi e – 2
n=
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2. Halogenation AE
ALKENES AND ALKYNES
Unsaturated HC
ALKENES 3. Hydrohalogenation
1. Ethylene/ethane
Symetrical
W/ Vinylic Carbon
4. Hydration/Acid-catalyzed hydration
Addition of water
2. Propene
Unsymetrical
ALKYNES
1. Ethyne/Acetylene
Terminal
Markonikov’s Rule:
The major product is the more stable one.
5. Mild Oxidation/Hydroxylation
Baeyer’s Test – test for
REACTION MECHANISM OF ALKENES (AE) alkenes with brown positive
Minus 1 – split – add result due to MnO2
6. Epoxidation
1. Hydrogenation/Saturation
Addition of H
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REACTION OF ALKYNES
1. Hydrogenation How are bonds oxidized?
o 1 available bond
o 2 available bonds
What bonds can be oxidized?
o Double bonds = 2 bonds
o Triple bond = 3 bonds
o Virylic H’s = 1 bond
o 2 – ketone
o 3 – acid
2. Halogenation o 4 -CO2
Practice Set 3
3. Hydrohalogenation
4. Hydration
a. Creation of enol
Alkyl + alcohol
Unstable
b. Tautomerization
Enol to keto form
Strong Oxidation/Oxidative Cleavage
Uses of KMnO4 in H+
Double or triple bonds are
completely broken
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Factors affecting Molecularity
ALKYL HALIDE
1. Nucleophile
Reactivity SN2 – strong: metal containing
a. Neuclophile substitution SN1 – weak: nonmetal/organic
b. Elimination
2. Substrate (a-carbon)
Elimination Reaction
a. Dehydrohalogenation
Reaction Stereochemistry
Molecularity of SN influences chiral
compounds
b. Dehydration SN1
o 50% retention + 50% inversion =
Racemization
Mix of R and S (racemic
mixture)
Ex
Omeprazole – R + S
R – less active
S – more active
“Resolution”
Esomeprazole (S-
omeprazole)
Thalidomide
R – therapeutic –
morning drug
S – teratogenic
Zaitsev’s Rule:
The major product is the more stable one.
Substitution
Molecularity
o Number of molecules involved in the SN2
first step o Almost 100% inversion or simply
inversion
SN mar occur in 2 ways o R to S; S to R
o RX + Nu -> RNu + X
o RX
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iv. Polyhydric/Polyols
ALCOHOL, ALDEHYDE, KETONE
Commonly from
Oxygen containing compounds carbohydrates
Ex. Sorbitol, mannitol
ALCOHOLS
ROH Aldehydes & Ketones
Weakly basic Carbonyl compounds
Extensive hydrogen bonding – RCOCH: aldehydes; can be further
azeotropic oxidized; have a reducing property;
RCOR: ketone;
Classification Ex.
a. Alpha-carbon
i. Primary Test
a. Aldehyde/Ketone: Tollen’s test – silver
mirror; Fehling’s test – brick-red
b. methyl ketones: iodoform test – yellow
ii. Secondary
ALDEHYDE
1. Vanillin
2. Benzaldehyde (bitter almond)
3. Formaldehyde
4. Glutaraldehyde
5. Paraldehyde
iii. Tertiary 6. Cinnamaldehyde (V.O.)
KETONE
1. Acetone
2. Pheromones
3. Testosterone
4. Ketone Volatile Oil
a. Camphor
b. Carvone – (-) spearmint
b. # of carbons
i. Monohydric
1 OH REDOX reaction
Ex. Methanol, ethanol
ii. Dihydric
2 OH (Diols/glycols)
Ex. Ethylene glycols,
propylene glycol
iii. Trihydric
3 OH
Ex. Gycerol/glycerin
1. Triglyceride/
Phospholipids
2. Nitroglycerin
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Non-REDOX Reaction 5. Grignard reaction
of aldehydes and ketone Grignard reagent (R-Mg+2-X-)
1-2 process
AN a. Formaldehyde/methanal – 1O
– H (Dehydrogenation/Oxidation)
+ H (Hydrogenation/Reduction)
1. Addition of H2O
b. Higher aldehyde - 2O
c. Ketones - 3O
2. Addition of HCN
CYANOHYDRIN
Precursor for amino acid
production
3. Addition of amines (1O)
Imine – double bonded amine;
schiff base
4. Addition of alcohols
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CARBOXYLIC ACID Reactions
1. Saponification
NaOH
2. Alcoholysis/Esterification
3. Amminolysis
Significant compounds
1. Benzoic acid – preservative 4. Anhydride Formation
2. Salicylic acid – keratolytic; precursor for
ASA
Whitfields ointment
(silang dalawa ni benzoic acid)
3. Valproic acid
anticonvulsant;enzyme inhibitor
4. Methylsalysilates/Oil of wintergreen 5. Conversion to acyl halides
analgesic
5. Acetylcholine
Neurotransmitter
6. Amino acids
Reactivities mechanism (SN acyl)
6. Hydrolysis
Any derivative + H2O = acid
(R to OH)
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