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
 Tri/tetra-substitution
 Follows cahn-ingold-prelog (CIP)
rules for prioritization
 High atomic number high priority
1. Hemolytic cleavage
 A-B = A. + B. (Free radicals) R.
 A-B = A- (Nu- nucleophile) + B+ (E+
electrophile)
 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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