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Pharmaceutical Organic Chemistry. 211 PHC lect.1 Dr. Ebtehal S AlAbdullah Textbooks: R. Fessenden and J. Fessenden, Organic Chemistry , PWS Publishers, Latest edition. Optional reading :

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Pharmaceutical organic chemistry

Pharmaceutical Organic Chemistry

211 PHC lect.1

Dr. Ebtehal S AlAbdullah

Pharmaceutical organic chemistry


R. Fessenden and J. Fessenden, Organic Chemistry, PWS Publishers, Latest edition.

Optional reading :

Joule and Smith, Heterocyclic Chemistry, Van Nostrand Reinhold, Latest edition.

Aim of the course

Aim of the Course

The Course is Designed to Provide the Students with:

  • Recognize the various classes and subclasses of organic compounds and how the chemical and physical properties influence their behavior.

  • Understand the chemical reactions unique to each class or subclass of organic molecules and their role in synthetic chemistry.

  • Recognize the different reaction mechanisms and their importance in synthesis.

  • Understand the stereochemistry of organic molecules and the stereochemical courses of organic reactions.

  • Understand the role of physicochemical properties, mechanisms, and stereochemistry of organic molecules in biology and pharmacy.

Topics to be covered

Topics to be covered:

Three parts:

Part one: Classes and Mechanism of reactions

a- Subsitiution

b- addition

c- elimination

d- rearrangement

e- Free radicals

Part two: Stereochemistry

Part three: Heterocyclic chemistry

Pharmaceutical organic chemistry


*Homework and Classroom Assignments and Discussion

Pharmaceutical organic chemistry

LEC. 1

  • Dr. Ebtehal al abdullah


Pharmaceutical Organic Chemistry

Part One:

Classes and Mechanisims of Organic reactions

Classes of organic compuonds and functional group

Classes of Organic compuondsand functional group

A functional group is an atom or a group of atoms with

characteristic chemical and physical properties. It is the

reactive part of the molecule.

Pharmaceutical organic chemistry

  • Reactions and Their Mechanisms

    • There are four general types of organic reactions

      • Substitutions

      • Additions

Pharmaceutical organic chemistry

  • Reactions and Their Mechanisms

    • Eliminations

    • Rearrangements

Pharmaceutical organic chemistry

  • Cleavage of Covalent Bonds

  • Homolytic cleavage: each atom involved in the covalent bond receives one electron, resulting in formation of free radical

  • Hetrolytic cleavage: both bonding electrons are retained by one of the atoms, resulting in formation of ionic species

Pharmaceutical organic chemistry

  • Heterolysis of Bonds to Carbons: Carbanions and Carbocations

    • Reaction can occur to give a carbocation or carbanion depending on the nature of Z

Pharmaceutical organic chemistry

  • Heterolysis of Bonds to Carbons: Carbanions and Carbocations

    • Carbocationshave only 6 valence electrons and a positive charge

    • Carbanions have 8 valence electrons and a negative charge

Pharmaceutical organic chemistry

  • Organic chemistry terms for Lewis acids and bases

    • Electrophiles(“electron-loving” reagents ): seek electrons to obtain a stable valence shell of electrons

      • Are electron-deficient themselves e.g. carbocations

    • Nucleophiles (“nucleus-loving” reagents): seek a proton or some other positively charged center

      • Are electron-rich themselves e.g. carbanions

1 substitution reactions

1- Substitution reactions

Substitution reaction in this type of reaction one atom ion or group is substituted for another

Substitution Reaction In this type of reaction one atom, ion, or group is substituted for another.

Its two types:

  • Nucleophilic Substitution Reaction

  • Electrophilic Substitution Reaction

Nucleophilic substitution reaction

Nucleophilic Substitution Reaction

Q: What is nucleophilic substitution reaction?

A species which has ability to donates a pair of electrons is termed as a nucleophile.

A reaction in which Nu is substituted by another Nu

can occur by an: a. SN1 path

b. SN2 path

Most common reaction of alkyl halides (RX) and alcohols (ROH)

Substitution reactions

Substitution reactions

The SN1 Mechanism

Nucleophilic substitution reaction of alkyl halide

Nucleophilic Substitution Reaction of alkyl halide

SN1 reaction

unimolecularnucleophilic substitution, two-step mechanism

Step1: ionization and formation of R+

Step2: combination of R+

Pharmaceutical organic chemistry

Cont. SN1 reaction

  • The rate of chemical reaction is a measure of how fast the reaction

  • proceed,

  • It dose not depend on the conc. Of Nu-, depend on only conc. Of RX

  • It follow first order kinetic, depend only on reactant conc.(RX)

  • It is nuimolecular reaction [ because only one particle (RX) is involved

  • in the transition state of rate determining step

Pharmaceutical organic chemistry

Cont. SN1 reaction

The rate-determinig step in SN1 reaction involves the formation of R+,

So, increasing the stability of R+ will increase the rate of the reaction

C6H5CH2+, CH2=CHCH2+, (CH3)3C+,(CH3)2CH+, CH3CH2+, CH3+

Decresing the stability of R+, decreasing SN1 rate of RX

* Only benzylic, allylic and 3°R+ undergo SN1

The s n 1 mechanism

The SN1 Mechanism


Pharmaceutical organic chemistry

Cont. SN1 reaction

When weak Nu such as H2O or ROH is used the rate of SN1 reaction

Is in the following order

C6H5CH2X > CH2=CHCH2X > 3° RX

When a strong Nu as CN- is used,

3° RX undergo SN1 reaction exclusively,where as


C6H5CH2X or



H2O or ROH



Pharmaceutical organic chemistry

Cont. SN1 reaction


Q1: List the following carbocation in order of increasing stability

Q2: Which of the following compounds is more reactive toward SN1

reaction. Explain why

1. C6H5CH2Br2. CH3Br 3. CH2=CHCH2Br

Substitution reactions1

Substitution reactions

The SN2 Mechanism

Pharmaceutical organic chemistry

Nucleophilic Substitution Reaction of alkyl halide

  • SN2 reaction

  • bimolecular nucleophilic substitution, one-step mechanism, which

  • involves a transition state.

  • Nu attacks from back-side.

  • Bimolecular reaction, because both Nu and RX are involved in the

  • transition state.

Transition state

Pharmaceutical organic chemistry

The Sn2 mechanism:

a) is a single step process

b) involves no intermediates

c) involves only one transition state, which is of low polarity

d) follows second order (bimolecular) kinetics. That is,


Pharmaceutical organic chemistry

Cont. SN2 reaction

  • The rate of second order, because it is proportional to conc. Of Nu & RX

  • Increase the steric hindrance around the halogenated carbon Decreases

  • the rate of SN2 reaction.

  • 3° RX are too hindered to undergo SN2 reaction.


  • increasing steric hindrance , decreasing SN2 rate

  • CH3X…… most reactive

  • 2 ° [R2CHX ]…… react slowly

  • 3 ° [R3X ] …….no react by SN2

  • When strong Nu as CN- is used, the SN2 rate in the following order

  • benzylic halide > Allylic halide > Methyl halide

  • ** CH3X and RCH2X (1° RX) undergo SN2 exclusively, irrespective of the

  • strength of Nu-

Pharmaceutical organic chemistry

Q: Outline all steps in the mechansim of each of the following reaction:

1. C6H5CH2Br + NaCN C6H5CH2CN + NaBr

2. C6H5CH2Br + H2O C6H5CH2OH + HBr

3. (CH3)3CCl + CH3O-Na+ (CH3)3COCH3 + NaCl

Summary of s n 1 s n 2 mechanisms

Summary of SN1 & SN2 Mechanisms


A bimolecular reaction

Back-side attack

2ed order in rate

Inversion of configuration

CH3X > 1oRX > 2oRX


A unimolecular reaction

An ionization reaction

1st order in rate

No inversion of configuration

3oRX > 2oRX

Summary of s n 1 s n 2 mechanisms1

Summary of SN1 & SN2 Mechanisms

Benzylic and allylic undergo both type of substitution

SN1 & SN2 Mechanisms

Depending on the strength of Nu

if weak Nu ……… SN1

if strong Nu ………. SN2

Linkage with the life sciences

Linkage with the life sciences

Information Enrichment

Medicall yspeaking pharmacology and drug design

MEDICALL YSPEAKINGPharmacology and Drug Design

Pharmacology is the study of how drugs interact with biological systems, including the mechanisms that explain drug action.

Pharmacology is a very important field of study because it serves as the basis for the design of new drugs.

Pharmaceutical organic chemistry


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