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CHEMISTRY
FOR PHARMACY
STUDENTS
C HEMISTRY
FOR PHARMACY
STUDENTS
General, Organic and
Natural Product Chemistry
Second Edition
LUTFUN NAHAR
Liverpool John Moores University
UK
SATYAJIT SARKER
Liverpool John Moores University
UK
This edition first published 2019
© 2019 John Wiley & Sons Ltd
Edition History
1e published 2007, ISBN 9780470017807
All rights reserved. No part of this publication may be reproduced, stored in a retrieval system, or transmitted, in any
form or by any means, electronic, mechanical, photocopying, recording or otherwise, except as permitted by law. Advice
on how to obtain permission to reuse material from this title is available at http://www.wiley.com/go/permissions.
The right of Lutfun Nahar and Satyajit Sarker to be identified as the authors of this work has been asserted in accor-
dance with law.
Registered Offices
John Wiley & Sons, Inc., 111 River Street, Hoboken, NJ 07030, USA
John Wiley & Sons Ltd, The Atrium, Southern Gate, Chichester, West Sussex, PO19 8SQ, UK
Editorial Office
The Atrium, Southern Gate, Chichester, West Sussex, PO19 8SQ, UK
For details of our global editorial offices, customer services, and more information about Wiley products visit us at
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Wiley also publishes its books in a variety of electronic formats and by print-on-demand. Some content that appears in
standard print versions of this book may not be available in other formats.
10 9 8 7 6 5 4 3 2 1
Dedicated to pharmacy students, from home
and abroad
Contents
Preface to the second edition xv
Preface to the first edition xvii
Chapter 1: Introduction 1
1.1 ole of Chemistry in Modern Life
R 1
1.2 Solutions and Concentrations 4
1.3 Suspension, Colloid and Emulsion 6
1.4 Electrolytes, Nonelectrolytes and Zwitterions 7
1.5 Osmosis and Tonicity 8
1.6 Physical Properties of Drug Molecules 10
1.6.1 Physical State 10
1.6.2 Melting Point and Boiling Point 10
1.6.3 Polarity and Solubility 11
1.7 Acid–Base Properties and pH 13
1.7.1 Acid–Base Definitions 14
1.7.2 Electronegativity and Acidity 18
1.7.3 Acid–Base Properties of Organic Functional Groups 19
1.7.4 pH, pOH and pKa Values 22
1.7.5 Acid–Base Titration: Neutralization 30
1.8 Buffer and its Use 32
1.8.1 Common Ion Effects and Buffer Capacity 34
vii
2.7 S ignificance of Chemical Bonding in Protein–Protein Interactions 63
2.8 Significance of Chemical Bonding in Protein–DNA Interactions 63
Chapter 3: Stereochemistry 65
3.1 S tereochemistry: Definition 66
3.2 Isomerism 66
3.2.1 Constitutional Isomers 66
3.2.2 Stereoisomers 67
3.3 Stereoisomerism of Molecules with More than One Stereocentre 82
3.3.1 Diastereomers and Meso Structures 82
3.3.2 Cyclic Compounds 84
3.3.3 Geometrical Isomers of Alkenes and Cyclic Compounds 85
3.4 Significance of Stereoisomerism in Determining Drug Action and Toxicity 88
3.5 Synthesis of Chiral Molecules 91
3.5.1 Racemic Forms 91
3.5.2 Enantioselective Synthesis 92
3.6 Separation of Stereoisomers: Resolution of Racemic Mixtures 93
3.7 Compounds with Stereocentres Other than Carbon 94
3.8 Chiral Compounds that Do Not Have Four Different Groups 94
viii Contents
4.5.3 Structure of Alkenes 167
4.5.4 Industrial uses of Alkenes 167
4.5.5 Preparations of Alkenes 168
4.5.6 Reactivity and Stability of Alkenes 168
4.5.7 Reactions of Alkenes 169
4.6 Alkynes and their Derivatives 169
4.6.1 Nomenclature of Alkynes 170
4.6.2 Structure of Alkynes 170
4.6.3 Acidity of Terminal Alkynes 171
4.6.4 Heavy Metal Acetylides: Test for Terminal Alkynes 171
4.6.5 Industrial Uses of Alkynes 172
4.6.6 Preparations of Alkynes 172
4.6.7 Reactions of Alkynes 172
4.6.8 Reactions of Metal Alkynides 174
4.7 Aromatic Compounds and their Derivatives 174
4.7.1 History 175
4.7.2 Definition: Hückel’s Rule 175
4.7.3 General Properties of Aromatic Compounds 175
4.7.4 Classification of Aromatic Compounds 176
4.7.5 Pharmaceutical importance of Aromatic
Compounds: Some Examples 177
4.7.6 Structure of Benzene: Kekulé Structure of Benzene 179
4.7.7 Nomenclature of Benzene Derivatives 183
4.7.8 Electrophilic Substitution of Benzene 184
4.7.9 Alkylbenzene: Toluene 190
4.7.10 Phenols 192
4.7.11 Aromatic Amines: Aniline 199
4.7.12 Polycyclic Benzenoids 207
4.8 Importance of Functional Groups in Determining Drug
Actions and Toxicity 209
4.8.1 Structure-Activity Relationships of Sulpha Drugs 210
4.8.2 Structure-Activity Relationships of Penicillins 211
4.8.3 Paracetamol Toxicity 213
4.9 Importance of Functional Groups in Determining
Stability of Drugs 213
Contents ix
5.3.3 Allylic Bromination 221
5.3.4 Radical Inhibitors 222
5.4 Addition Reactions 223
5.4.1 Electrophilic Additions to Alkenes and Alkynes 223
5.4.2 Symmetrical and Unsymmetrical Addition to Alkenes and Alkynes 226
5.4.3 Nucleophilic Addition to Aldehydes and Ketones 240
5.5 Elimination Reactions: 1,2-Elimination or β-Elimination 254
5.5.1 E1 Reaction or First Order Elimination 255
5.5.2 E2 Reaction or Second Order Elimination 256
5.5.3 Dehydration of Alcohols 257
5.5.4 Dehydration of Diols: Pinacol Rearrangement 259
5.5.5 Base-Catalysed Dehydrohalogenation of Alkyl Halides 260
5.6 Substitution Reactions 265
5.6.1 Nucleophilic Substitutions 266
5.6.2 Nucleophilic Substitutions of Alkyl Halides 273
5.6.3 Nucleophilic Substitutions of Alcohols 276
5.6.4 Nucleophilic Substitutions of Ethers and Epoxides 282
5.6.5 Nucleophilic Acyl Substitutions of Carboxylic Acid Derivatives 286
5.6.6 Substitution Versus Elimination 293
5.7 Electrophilic Substitutions 294
5.7.1 Electrophilic Substitution of Benzene 294
5.8 Hydrolysis 300
5.8.1 Hydrolysis of Carboxylic Acid Derivatives 300
5.9 Oxidation–Reduction Reactions 305
5.9.1 Oxidizing and Reducing Agents 305
5.9.2 Oxidation of Alkenes 305
5.9.3 Oxidation of Alkynes 307
5.9.4 Hydroxylation of Alkenes 307
5.9.5 Oxidative Cleavage of syn-Diols 308
5.9.6 Ozonolysis of Alkenes 308
5.9.7 Ozonolysis of Alkynes 309
5.9.8 Oxidation of Alcohols 309
5.9.9 Oxidation of Aldehydes and Ketones 311
5.9.10 Baeyer–Villiger Oxidation of Aldehydes or Ketones 312
5.9.11 Reduction of Alkyl Halides 312
5.9.12 Reduction of Organometallics 312
5.9.13 Reduction of Alcohols via Tosylates 313
5.9.14 Reduction of Aldehydes and Ketones 313
5.9.15 Clemmensen Reduction 315
5.9.16 Wolff–Kishner Reduction 316
5.9.17 Reduction of Acid Chlorides 316
5.9.18 Reduction of Esters 317
x Contents
5.9.19 Hydride Reduction of Carboxylic Acids 318
5.9.20 Reduction of Oximes or Imine Derivatives 318
5.9.21 Reduction of Amides, Azides and Nitriles 319
5.9.22 Reductive Amination of Aldehydes and Ketones 320
5.10 Pericyclic Reactions 320
5.10.1 Diels–Alder Reaction 320
5.10.2 Essential Structural Features for Dienes and Dienophiles 321
5.10.3 Stereochemistry of the Diels–Alder Reaction 322
5.10.4 Sigmatropic Rearrangements 323
5.10.5 Hydrogen Shift 323
5.10.6 Alkyl Shift: Cope Rearrangement 324
5.10.7 Claisen Rearrangement 324
Contents xi
6.8 Q uinoline and Isoquinoline 354
6.8.1 Physical Properties of Quinoline and Isoquinoline 354
6.8.2 Preparations of Quinoline and Isoquinoline 355
6.8.3 Reactions of Quinoline and Isoquinoline 357
6.9 Indole 358
6.9.1 Physical Properties of Indole 359
6.9.2 Preparations of Indole 359
6.9.3 Reactions of Indole 360
6.9.4 Test for Indole 361
xii Contents
8.3.9 Miscellaneous Carbohydrates 426
8.3.10 Cell Surface Carbohydrates and Blood Groupings 428
8.4 Glycosides 429
8.4.1 Biosynthesis of Glycosides 430
8.4.2 Classification 430
8.4.3 Test for Hydrocyanic Acid (HCN) 432
8.4.4 Pharmaceutical Uses and Toxicity 432
8.4.5 Anthracene/Anthraquinone Glycosides 433
8.4.6 Isoprenoid Glycosides 436
8.4.7 Iridoid and Secoiridoid Glycosides 440
8.5 Terpenoids 442
8.5.1 Classification 442
8.5.2 Biosynthesis of Terpenoids 443
8.5.3 Monoterpenes 445
8.5.4 Sesquiterpenes 446
8.5.5 Diterpenes 455
8.5.6 Triterpenes 461
8.5.7 Tetraterpenes 465
8.6 Steroids 466
8.6.1 Structures of Steroids 467
8.6.2 Stereochemistry of Steroids 468
8.6.3 Physical Properties of Steroids 468
8.6.4 Types of Steroid 469
8.6.5 Biosynthesis of Steroids 471
8.6.6 Synthetic Steroids 472
8.6.7 Functions of Steroids 473
8.7 Phenolics 476
8.7.1 Phenylpropanoids 477
8.7.2 Coumarins 478
8.7.3 Flavonoids and Isoflavonoids 481
8.7.4 Lignans 486
8.7.5 Tannins 489
Index 493
Contents xiii
Preface
to the second
edition
The first edition of Chemistry for Pharmacy Students: General, Organic and Natural
Product Chemistry was written to address the need for the right level and appro-
priate coverage of chemistry in any modern Pharmacy curricula. The first edition
reflected on the changing face of Pharmacy profession and the evolving role of
pharmacists in the modern healthcare systems, and was aimed at placing chem-
istry more in the context of medicines and patients. Since the publication in 2007,
in subsequent years, the first edition has been translated into the Greek, Japanese
and Portuguese languages, and has acclaimed huge acceptance and popularity
among Pharmacy students, as well as among academics who teach chemistry in
Pharmacy curricula all over the world.
It has been over a decade since the publication of the first edition. We feel
that it has now become necessary to compile a second edition, which should be a
thoroughly revised and enhanced version of the first. The second edition will also
cater for the chemistry requirements in any ‘Integrated Pharmacy Curricula’, where
science in general is meant to be taught ‘not in isolation’, but together with, and
as a part of, other practice and clinical elements of Pharmacy curricula. Whatever
may be the structure and content of any Pharmacy curriculum, there will always be
two fundamental aspects in it – medicines (drugs) and patients.
Pharmacy began its journey as a medicine (drug)-focused science subject but,
over the years, it has evolved as a more patient-focused subject. Irrespective of
the focus, the need for chemistry knowledge and understanding in any Pharmacy
curricula cannot be over-emphasized. We know that all drugs are chemicals. The
ways any drug exerts its pharmacological actions and also toxicity in a patient are
governed by a series of biochemical reactions. Therefore, chemistry knowledge
and understanding are fundamental to any Pharmacy programme, which is essen-
tially the study of various aspects of drugs, their applications in patients, patient
care and overall treatment outcome.
Like the first edition, this revised, reorganized and significantly enhanced sec-
ond edition covers all core topics related to general, organic and natural product
chemistry currently taught in Pharmacy undergraduate curricula in the UK, USA
xv
and various other developed countries, and relates these topics to drug molecules,
their development and their fate once given to patients. While the second edition
still provides a concise coverage of the essentials of general, organic and natural
product chemistry into a manageable, affordable and student-friendly text, by con-
centrating purely on the basics of various topics without going into exhaustive
detail or repetitive examples, the first chapter, which deals with various properties
of drug molecules, has been significantly ‘beefed up’ in this second edition. Gen-
erally, the contents of the second edition are organized and dealt with in a similar
way, to the first to ensure that the contents are suitable for year 1 (level 4) and
year 2 (level 5) levels of most of the Pharmacy curricula. Theoretical aspects have
been covered in the context of applications of these theories in relation to drug
molecules, their discovery and developments.
Chapter 1 presents an account of general aspects of chemistry and their contri-
butions to modern life, with particular emphasis on modern medicine and discus-
sions on various important properties of drug molecules, for example, pH, polarity
and solubility; it also covers some related fundamental concepts like electrolytes,
zwitterion, osmosis, tonicity and so on. Chapter 2 incorporates the fundamentals
of atomic structure and bonding and discusses the relevance of chemical bonding
in drug molecules and drug–receptor interactions, while Chapter 3 covers key
aspects of stereochemistry with particular focus given on the significance of ste-
reoisomerism in determining drug action and toxicity. Chapter 4 deals with organic
functional groups, their preparations, reactions and applications. All major types
of organic reactions and their importance in drug discovery, development, delivery
and metabolism in patient’s body are outlined in Chapter 5. Chapter 6 is about het-
erocyclic compounds; their preparations, reactions and applications. While nucleic
acids are covered in Chapter 7, various aspects of natural products including the
origins, chemistry, biosynthesis and pharmaceutical importance of alkaloids, car-
bohydrates, glycosides, iridoids and secoiridoids, phenolics, steroids and terpe-
noids are presented in Chapter 8.
Although the primary readership of the second edition still remains to be the
Pharmacy undergraduate students (BPharm/MPharm), especially in their first and
second years of study, further readership can come from the students of various
other subject areas within Biomedical Science and the Food Sciences, Life Sciences
and Health Sciences, where the basic chemistry knowledge is essential for their
programmes.
Dr Lutfun Nahar
Professor Satyajit Sarker
xvii
the students, but none of them can meet the demand of the recent changes in
Pharmacy courses in the developed countries. Therefore, there has been a press-
ing need for a chemistry text covering the fundamentals of general, organic and
natural products chemistry written at a correct level for the Pharmacy undergrad-
uates. Physical (Preformulation) and Analytical Chemistry (Pharmaceutical Anal-
ysis) are generally taught separately at year 2 and year 3 levels of any modern
MPharm course, and there are a number of excellent and up-to-date texts available
in these areas.
During our teaching careers, we have always struggled to find an appropriate
book that can offer general, organic and natural products chemistry at the right
level for pharmacy undergraduate students, and address the current changes in
Pharmacy curricula all over the world, at least in the UK. We have always ended up
recommending several books and also writing notes for the students. Therefore,
we have decided to address this issue by compiling a chemistry book for Pharmacy
students, which will cover general, organic and natural product chemistry in rela-
tion to drug molecules. Thus, the aims of our book are to provide the fundamental
knowledge and overview of all core topics related to general, organic and natural
product chemistry currently taught in pharmacy undergraduate courses in the
UK, USA and various other developed countries, relate these topics to the better
understanding of drug molecules and their development, and meet the demand
of the recent changes in pharmacy curricula. This book attempts to condense the
essentials of general, organic and natural product chemistry into a manageable,
affordable and student-friendly text, by concentrating purely on the basics of var-
ious topics without going into exhaustive detail or repetitive examples.
In Pharmacy undergraduate courses, especially in the UK, we get students of
heterogeneous educational backgrounds; while some of them have very good
chemistry background, the others have the bare minimum or not at all. From our
experience in teaching Pharmacy undergraduate students, we have been able
to identify the appropriate level that is required for all these students to learn
properly. While we recognise that learning styles and levels vary from student
to student, we can still try to strike the balance in terms of the level and stan-
dard at a point, which is not too difficult or not too easy for any students, but
will certainly be student-friendly. Bearing this in mind, the contents of this book
are organised and dealt with in a way that they are suitable for year 1 and year 2
levels of pharmacy curriculum. While the theoretical aspects of various topics are
covered adequately, much focus has been given to the applications of these the-
ories in relation to drug molecules, their discovery and developments. Chapter 1
provides an overview of some general aspects of chemistry and their importance
in modern life, with particular emphasis on medicinal applications, and brief dis-
cussions on various physical characteristics of drug molecules, e.g. pH, polarity,
and solubility. While Chapter 2 deals with the fundamentals of atomic structure
and bonding, Chapter 3 covers various aspects of stereochemistry. Chapter 4
incorporates organic functional groups, and various aspects of aliphatic, aromatic
Chemistry for Pharmacy Students: General, Organic and Natural Product Chemistry,
Second Edition. Lutfun Nahar and Satyajit Sarker.
© 2019 John Wiley & Sons Ltd. Published 2019 by John Wiley & Sons Ltd.
all are possible due to chemistry. It has played a major role in pharmaceutical
advances, forensic science and modern agriculture. Diseases and their remedies
have also been a part of human lives. Chemistry plays an important role in under-
standing diseases and their remedies; that is, drugs.
Medicines or drugs that we take for the treatment of various ailments are chem-
icals, either organic or inorganic molecules. However, most drugs are organic mole-
cules. These molecules are either obtained from natural sources or synthesized in
chemistry laboratories. Some important drug molecules are discussed here.
Aspirin, an organic molecule, is chemically known as acetyl salicylic acid and
is an analgesic (relieves pain), antipyretic (reduces fever) and anti-inflammatory
(reduces swelling) drug. Studies suggest that aspirin can also reduce the risk
of heart attack. It is probably the most popular and widely used analgesic drug
because of its structural simplicity and low cost. Salicin is the precursor of aspirin.
It is found in the willow tree bark, whose medicinal properties have been known
since 1763. Aspirin was developed and synthesized in order to avoid the irritation
in the stomach caused by salicylic acid, which is also a powerful analgesic, derived
from salicin. In fact, salicin is hydrolysed in the gastrointestinal tract to produce
D-glucose and salicyl alcohol (see Section 8.4). Salicyl alcohol, on absorption, is
oxidized to salicylic acid and other salicylates. However, aspirin can easily be syn-
thesized from phenol using the Kolbe reaction (see Section 4.7.10.6).
OH OH O OH O OH
O-Glucosyl OH OH O
O
O
H
OH N
NH2 OH
4-Aminophenol Paracetamol
Acetaminophen
COOH
HO
CH2 C
H
NH2
O
OH N
H
OH HO H CH3
(L)-Dopa Morphine
(The precursor of dopamine)
H H
H H H H
N N S
S O
N O N
O O
O
COOH H
COOH
Penicillin G Penicillin V
(The first penicillin of the penicillin Phenoxymethylpenicillin
group of antibiotics)
Chapter 1: Introduction 3
nalgesic and antipyretic, paracetamol, and semisynthetic, such as penicillin
a
V. Whatever the source is, chemistry is involved in all processes in the discovery
phase. For example, if a drug molecule has to be purified from a natural source,
for example, plant, the processes like extraction, isolation and identification are
used, and all these processes involve chemistry (see Section 8.1.3.1).
Similarly, in the drug development steps, especially in pre-formulation and for-
mulation studies, the structures and the physical properties (e.g. solubility and
pH), of the drug molecules are exploited. Chemistry, particularly physical prop-
erties of drugs, is also important to determine storage conditions. Drugs having
an ester functionality, for example, aspirin, could be quite unstable in the presence
of moisture and should be kept in a dry and cool place. The chemistry of drug mol-
ecules dictates the choice of the appropriate route of administration. Efficient
delivery of drug molecules to the target sites requires manipulation of various
chemical properties and processes; for example, microencapsulation, nanopar-
ticle-aided delivery and so on. When administered, the action of a drug inside
our body depends on its binding to the appropriate receptor and its subsequent
metabolic processes, all of which involve complex enzyme-driven biochemical
reactions.
All drugs are chemicals, and pharmacy is a subject that deals with the study of
various aspects of drugs. Therefore, it is needless to say that to become a good
pharmacist the knowledge of the chemistry of drugs is essential. Before moving on
to the other chapters, let us try to understand some of the fundamental chemical
concepts in relation to the physical properties of drug molecules (see Section 1.6).
Chapter 1: Introduction 5
crystals, resulting in a saturated solution. The equilibrium of a solution depends
on the temperature.
A stock solution is prepared with a known concentration, from which a diluted
solution can be made. The process of adding more solvent to a solution or removing
some of the solute is called dilution. In other words, dilution is the process of
reducing the concentration of a solute in solution, usually simply by mixing with
more solvent. Any unit can be used for both volume and concentration as long as
they are the same on both sides of the equation. The concentration of the diluted
solution can easily be calculated from the following equation:
C1V1 C2V2
Where, C1 and C2 are the initial and final concentrations and V1 and V 2 are the initial
and final volumes of the solution.
A serial dilution, often used in various in vitro assays, is simply a series of simple
dilutions. Serial dilutions are made in increments of 1000 (103), 100 (102), 10 (10-
fold) or 2 (twofold), but 10-fold and twofold serial dilutions are commonly used.
Serial dilutions are an accurate method of making solutions of low molar concen-
trations. The first step in making a 10-fold serial dilution is to take stock solution
(1 ml) in a tube and then to add distilled water (9 ml) or other suitable solvents. For
making a twofold serial dilution one should take stock solution (1 ml) in a tube and
then add distilled water (1 ml) or other suitable solvents.
Chapter 1: Introduction 7
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