Heterocycles in life and society an introduction to heterocyclic chemistry biochemistry and applications second edition

Heterocycles in Life and Society

Heterocycles in Life and Society: An Introduction to Heterocyclic Chemistry, Biochemistry and Applications,
Second Edition. Alexander F. Pozharskii, Anatoly T. Soldatenkov and Alan R. Katritzky.
© 2011 John Wiley & Sons, Ltd. Published 2011 by John Wiley & Sons, Ltd. ISBN: 978-0-470-71411-9


Heterocycles in Life
and Society
An Introduction to Heterocyclic Chemistry,
Biochemistry and Applications
Second Edition

by
ALEXANDER F. POZHARSKII
Soros Professor of Chemistry, Southern Federal University,
Russia
ANATOLY T. SOLDATENKOV
Professor of Chemistry, Russian People’s Friendship University,
Russia
ALAN R. KATRITZKY
Kenan Professor of Chemistry, University of Florida, Gainesville,
USA

A John Wiley & Sons, Ltd., Publication


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Library of Congress Cataloging-in-Publication Data
Pozharskii, A. F. (Aleksandr Fedorovich)

Heterocycles in life and society / Alexander F. Pozharskii, Alan R. Katritzky, Anatoly Soldatenkov. – 2nd ed.
p. cm.
ISBN 978-0-470-71411-9 (hardback) – ISBN 978-0-470-71410-2 (paper)
1. Heterocyclic chemistry. I. Katritzky, Alan R. II. Soldatenkov, A. T. (Anatoly Timofeevich) III. Title.
QD400.P6713 2011
547 .59 – dc22
2010054024
A catalogue record for this book is available from the British Library.
Print ISBN: 978-0-470-71411-9 (H/B) 978-0-470-71410-2 (P/B)
ePDF ISBN: 978-1-119-99838-9
oBook ISBN: 978-1-119-99837-2
ePub ISBN: 978-1-119-97013-2
eMobi ISBN: 978-1-119-97014-9
Typeset in 9/11pt Times Roman by Laserwords Private Limited, Chennai, India
Printed in Great Britain by Antony Rowe Ltd, Chippenham, Wiltshire


Contents

Preface to Second English Edition
Preface to First English Edition
1.

Molecular Rings Studded With Jewels
1.1
From Homocycle to Heterocycle
1.2
Building Heterocycles From Benzene
1.3
Some More Kinds of Heterocycles

1.4
Problems
1.5
Suggested Reading

2.

Why
2.1
2.2
2.3
2.4

2.5
2.6
2.7

Nature Prefers Heterocycles
Reactions for all Tastes
Heterocycles as Acids and Bases
Heterocycles and Metals
‘There are Subtle Ties of Power. . .’
2.4.1
The van der Waals-London Interactions
2.4.2
Hydrogen Bonding
2.4.3
Electrostatic Interactions
2.4.4
Molecular Complexes

2.4.5
Hydrophobic Forces
Tautomerism: Heterocycles and Their ‘Masks’
Problems
Suggested Reading

ix
xiii
1
1
2
6
8
8
11
11
14
15
17
18
19
21
21
25
27
31
33

3.

Heterocycles and Hereditary Information
3.1
Nucleic Acids
3.2
The Double Helix
3.3
How One DNA Doubles Itself
3.4
Protein Synthesis, Genetic Code and the Genome
3.5
What are Mutations?
3.6
Mysterious Telomeres
3.7
Gene Expression
3.8
Problems
3.9
Suggested Reading

35
35
38
42
45
50
54
55
60
61

4.

Enzymes, Coenzymes and Vitamins
4.1
Molecular Robots
4.2
Coenzymes and Enzymes as ‘Joint Molecular Ventures’

63
63
66


vi

Contents

4.3
4.4
4.5
4.6

4.2.1
Oxidative–Reductive Coenzymes
4.2.2
Coenzymes as Carriers of Molecular Species
Vitamins, the ‘Molecules of Health’
Ribozymes: Vestiges of an Ancient World
Problems

Suggested Reading

67
78
97
99
103
104

5.

Heterocycles and Bioenergetics
5.1
ATP as the Universal Currency of Energy
5.2
Breathing
5.2.1
Glycolysis
5.2.2
The Krebs Cycle, or the ‘Molecular Merry-Go-Round’
5.2.3
The Respiratory Chain
5.3
Problems
5.4
Suggested Reading

107
108
111

112
115
118
122
123

6.

Heterocycles and Photosynthesis
6.1
Chlorophyll: Sunlight-Receiving Antenna and Energy Carrier
6.2
What Daylight can Achieve
6.3
Photosynthesis Without Light
6.4
Problems
6.5
Suggested Reading

125
126
130
135
138
138

7.

Heterocycles and Health

7.1
Medicines From a Natural Storehouse
7.2
Heterocycles Versus Infectious Microbes
7.2.1
In Search of ‘Magic Bullets’
7.2.2
Sulfanilamides and Heterocycles
7.2.3
Antibiotics
7.2.4
Antibiotics From the Ocean’s Depths
7.2.5
Heterocyclic Antifungal Agents
7.2.6
Heterocycles Against Parasitic Diseases
7.3
Heterocycles and Viral Infections
7.4
Heterocycles and the Diseases of Our Century
7.4.1
Heterocycles to Cure Stress, Brain Disorders and Pain
7.4.2
Heterocycles and Cardiovascular Diseases
7.4.3
Heterocycles and Malignant Tumors
7.5
Heterocyclic Molecules in Combat with Ulcers and Sexual Dysfunctions
7.6
Problems

7.7
Suggested Reading

139
139
143
143
144
146
152
155
155
158
162
163
169
173
178
181
182

8.

Heterocycles in Agriculture
8.1
A Century of Chemical Warfare Against Weeds
8.2
Regulators of Plant Growth
8.3
The Struggle Against Voracious Insects

8.4
Resisting the Kingdoms of Mustiness and Rot
8.5
Heterocycles in Animal Husbandry
8.6
Combinatorial Chemistry and Functional Genomics in the Synthesis
of Biologically Active Heterocyclic Compounds

185
186
190
193
200
202
202


Contents
8.7
8.8
9.

Problems
Suggested Reading

Heterocycles in Industry and Technology
9.1
Heterocycles and Natural Colors
9.2
Dyes

9.2.1
From Imperial Cloaks to Jeans
9.2.2
‘Cyanine’ Means Azure
9.2.3
Phthalocyanines: Sometimes Better than Porphyrins
9.2.4
The Anchoring of Dyes
9.3
Fluorescent Agents
9.3.1
Why They Shine
9.3.2
Safety and Aesthetics
9.3.3
How to Convert White into Snow White
9.3.4
Markers and Tracers
9.3.5
Imaging and Diagnostic Agents
9.3.6
Lasers Containing Heterocyclic Luminophores
9.4
Color Change Compounds
9.5
Fire Retardancy
9.6
Photographic Materials and Recorders of Information
9.7
Heterocycles as Food Additives

9.8
Heterocycles as Cosmetics and Perfumery Ingredients
9.9
Other Applications
9.10 Problems
9.11 Suggested Reading

vii
205
207
209
209
211
211
214
215
217
218
218
219
220
221
222
226
231
233
235
237
241
243

245
246

10. Heterocycles and Supramolecular Chemistry
10.1 Molecular Recognition and Host–Guest Interactions
10.1.1 Cation Receptors
10.1.2 Anion-, Betaine- and Ionic Associated Receptors
10.1.3 Receptors for Neutral Molecules
10.1.4 Molecular Carcerands
10.1.5 Molecular Containers for the Proton
10.2 Self-Assembling Molecular Systems
10.3 Problems
10.4 Suggested Reading

247
248
248
257
259
261
262
267
272
274

11. Heterocycles and Twenty-First Century Challenges
11.1 Energy Problem
11.1.1 Biofuels
11.1.2 Hydrogen as a Fuel
11.1.3 Direct Use of Solar Energy

11.1.4 Conducting Materials
11.2 Ecology and Green Chemistry
11.3 Biotechnology and Related Problems
11.3.1 Enzyme Technologies
11.3.2 DNA Technologies
11.3.3 New Trends in Health Care
11.3.4 Heterocycles as Molecular Sensors

275
275
275
276
278
286
293
299
299
304
309
310


viii

Contents
11.4
11.5
11.6

From Molecular Devices to Molecular Computer

Problems
Suggested Reading

315
321
322

12. The Origin of Heterocycles
12.1 The Origin of the Universe and the Appearance of Chemical Elements
12.2 Interstellar Molecules
12.3 Organic Compounds in Comets and Meteorites
12.4 Do Heterocycles Exist on the Moon and Mars?
12.5 The Atmosphere of Earth and Other Planets
12.6 Heterocycles and the Origin of the Biosphere
12.6.1 Simple Precursors of Heterocycles
12.6.2 Heterocyclic Amino Acids
12.6.3 Pyrroles and Porphyrins
12.6.4 Furanose Sugars
12.6.5 Nicotinamide
12.6.6 Purines and Pyrimidines
12.6.7 Nucleosides and Nucleotides
12.6.8 Polynucleotides and the Birth of ‘Animated’ Organic Molecules
12.7 Problems
12.8 Suggested Reading

325
326
328
333
335

335
336
336
338
340
341
344
344
345
350
358
358

Conclusion
Answers and References to Selected Problems
Index

361
363
371


Preface to Second English Edition

On 7 September 2009, Chemical Abstracts Service registered its 50-millionth chemical
substance – a heterocyclic compound of the following structure:
O
N
S

HO

N

N CH
3

F

Hardly a casual coincidence: heterocyclic compounds form the largest and one of the most
important classes of organic compounds and some 55% of organic chemistry publications include
the field. They include not only the many thousands of original articles and conference materials published annually but a great number of scientific monographs such as the multivolume
Comprehensive Heterocyclic Chemistry, covering all fields of heterocyclic chemistry. Heterocyclic
chemistry is taught worldwide at most universities and its scope is reflected in many fine text compendia and reference sources. It is therefore very strange that many general chemistry (and even
organic chemistry) texts fail to include heterocycles and discuss the significance of their chemistry,
or at most only in a nonsystematic manner. Furthermore, time constraints often prevent teachers
of chemistry from elaborating on the manifold applications of heterocycles. This is why from the
very beginning the main goal of the present book and its predecessor was to bridge this gap and to
emphasize not so much the innumerable reactions of the different classes of heterocycles as their
practical importance in life and society, especially their scientific applications in various branches
of technology, medicine and agriculture. Our hope was, and is, that this approach will inspire the
student to become involved in an immensely important and exciting field of modern chemical
science and technology. The 14 years that have passed since the first edition have justified this
approach. Indeed, human society, in addition to chronic old problems, now faces acute, newly
recognized dangers such as climate change and ecology degradation, energy shortages, depletion
of mineral resources, population growth, pandemic illnesses and so on. These challenges have
forced science to become more applied and expensive but at the same time more productive and
useful. This productivity results from the appearance of new powerful physical methods, apparatus
as well as fundamental developments in computational techniques.
The past 10 years have been marked in biochemistry by such milestone achievements as

genome decoding, clarification of ribosome structure and its activity mechanism, and wide applications of imaging techniques. Further progress has been made in medicinal chemistry where
new methods of biological screening, drug delivery and drug targeting in combination with


x

Preface to Second English Edition

innovative chemotherapy have been elaborated. An epochal event in science is the creation of
nanotechnology which, via new materials and electronic devices, is leading to revolutionary
changes in our future life. In the energy sector the growing production of biofuels, progress
in development of hydrogen as a fuel, artificial photosynthesis and dye-sensitized solar cells all
look very encouraging. These and other lines of development would be impossible without organic
chemistry and often without heterocyclic compounds. The discussion of these themes lies at the
focus of this second edition: most chapters have been substantially revised and updated, and
chapter 11 is completely new.
While this book is intended for university level chemistry and biochemistry students and their
instructors, it should be of interest to researchers over the whole of the chemical, biological,
medical and agricultural sciences as well as in adjacent branches of science and technology.
These assertions are well founded because the majority of known pharmaceutical preparations
(antibiotic, neurotropic, cardiovascular, anticarcinogenic) are heterocyclic in nature; because the
agricultural use of new plant development regulators and pesticides based on heterocyclic structures
becomes more widespread each year; and because great attention is being paid to the synthesis and
production of new kinds of thermostable polymers, highly durable fibers, fast pigments, colorants
and functional dyes and of organic conductors containing heterocyclic fragments.
This book consists of 12 chapters. First, chapters (1) and (2) present the elements of the
structure and properties of heterocycles and are a useful introduction to the fundamentals of
their chemistry. Next, four chapters deal in a general way with the key role of heterocyclic
molecules in life processes, including the transfer of hereditary information (3), the manner in
which enzymes function (4), the storage and transfer of bioenergy (5) and photosynthesis (6).

Chapters (7)–(9) consider the applications of heterocycles in medicine, agriculture, and industry,
respectively. We have now dedicated chapter (10) to supramolecular chemistry in view of its
significance. Finally, chapter (11) considers the future contribution of heterocyclic chemistry to
modern trends of applied science, the latest discoveries and the prospects of finding new spheres of
use for heterocycles. Chapter (12) deals with the past: specifically the emergence of heterocyclic
molecules on primordial Earth, which is tightly connected with the far-reaching achievements
of astrophysics. Due to modern orbital telescopes and space stations our knowledge about the
origin of the Universe and its evolution has been significantly widened and deepened. On this
basis new scientific disciplines are arising and strongly developing. In two of these, perhaps the
most fascinating (prebiotic chemistry, synthetic biology), the role of heterocyclic compounds is
especially important. In fact, a test-tube recreation of the process of molecular evolution up to
synthesis of biological cells and live organisms is put forward as a not so distant perspective. It is
not necessary to possess a rich imagination to foresee that the consequences of such a development
of events could be even more dramatic then that of nanotechnology.
Throughout this text the student will learn to apply the knowledge gained by working on
problems related to the topics covered in each chapter. Many of the 100 problems have been
chosen from scientific journals and represent areas of recent significant interest. The scientists
who solved these mysteries were yesterday’s students. Thus, the approach to the problems will
give today’s students further insight into nature and a preview of what is scientifically possible.
Each chapter also contains suggested further reading.
The authors have tried to organize this book in as simplified a form as possible, in as far as the
scientific language is concerned. Each chapter is preceded by a piece written by a Russian poet
(translated into English by E. N. Sokolyuk) or (in one case) an American poet. The selected verses
may suggest subtle links with the concepts and contents of each chapter and were introduced with
the hope of fruitful cross-pollination between the natural sciences and humanities, so much needed
in our modern world.


Preface to Second English Edition

xi

In conclusion, we would like to express our warm acknowledgements to many people who
helped us during the preparation of the second edition of this book. We are most grateful for
helpful discussion and technical assistance from Dr Anna Gulevskaya, Dr Valery Ozeryanskii (for
reading Chapter 11), Dr Vladimir Sorokin (who kindly supplied us with some fresh literature
sources) and Dr John Zoltewicz.
A. F. Pozharskii
A. T. Soldatenkov
A. R. Katritzky


Preface to First English Edition

N
The book presents an updated translation of the Russian original ‘MoJIekyJIbI-IIepcTH ’ by A. F.
Pozharskii and A. T. Soldatenkov, published in 1993 by Khimiya. It has been a great pleasure
to accept the invitation of my long-standing friend Sasha Pozharskii to join him and Professor
Soldatenkov in producing the present English version, which follows closely the concepts and
objectives of the original. We hope that this book may ignite for its readers some of the passion for
heterocyclic chemistry which we the authors possess and help to repair the neglect of heterocyclic
chemistry on the US academic scene. This neglect contrasts with the high importance awarded
to heterocyclic chemistry and biochemistry by American industry, as well as by academic and
industrial chemists alike in Europe, Japan and all over the world.
This volume could not have been produced without the help of many people. Dr Daniel Brown
(Cambridge) read the whole text and made very helpful suggestions. Among many other colleagues
who read parts of the work, I would like to acknowledge particularly Dr Phil Cote, Dr Alastair
Monro, Dr Emil Pop, Dr Nigel Richards, Dr Eric Scriven and Dr John Zoltewicz. It is a pleasure
to thank also Ms Jacqui Wells, Dr Olga Denisko and Ms Cynthia Lee for all the help they gave
me in producing and finalizing the manuscript.

Alan R. Katritzky
Gainesville, Florida
April 1996


1
Molecular Rings Studded With Jewels
Fortune Goddess, in your glory, in your honor, stern Kama,
Bangles, finger-rings and bracelets I will lay before your Temple.
V. Bryusov

Readers of this book, whether or not they are students of organic chemistry, will all be aware
of the vital role of proteins, fats and carbohydrates in life processes. Experience has shown
that considerably less is usually known about another class of compounds which have a similar
importance in the chemistry of life, namely the heterocyclic compounds or, in short, heterocycles.
What are heterocycles?

1.1

From Homocycle to Heterocycle

It is rumored that the Russian scientist Beketov once compared heterocyclic molecules to jewelry
rings studded with precious stones. Several carbon atoms thus make up the setting of the molecular
ring, while the role of the jewel is played by an atom of another element, a heteroatom. In general,
it is the heteroatom which imparts to a heterocycle its distinctive and sometimes striking properties.
For example, if we change one carbon atom in cyclohexane for one nitrogen atom, we obtain a
heterocyclic ring, piperidine, from a homocyclic molecule. In the same way, we can derive pyridine
from benzene, or 1,2,5,6-tetrahydropyridine from cyclohexene (Figure 1.1).
A great many heterocyclic compounds are known. They differ in the size and number of their

rings, in the type and number of heteroatoms, in the positions of the heteroatoms and so on. The
rules of their classification help to orient us in this area.
Cyclic hydrocarbons are divided into cycloalkanes (cyclopentane, cyclohexane, etc.), cycloalkenes (e.g., cyclohexene) and aromatic hydrocarbons (with benzene as the main representative).
The most basic general classification of heterocycles is similarly divided into heterocycloalkanes
(e.g., piperidine), heterocycloalkenes (e.g., 1,2,5,6-tetrahydropyridine) and heteroaromatic
systems (e.g., pyridine, etc.). Subsequent classification is based on the type of heteroatom. On
the whole, heterocycloalkanes and heterocycloalkenes show comparatively small differences
when compared with related noncyclic compounds. Thus, piperidine possesses chemical
Heterocycles in Life and Society: An Introduction to Heterocyclic Chemistry, Biochemistry and Applications,
Second Edition. Alexander F. Pozharskii, Anatoly T. Soldatenkov and Alan R. Katritzky.
© 2011 John Wiley & Sons, Ltd. Published 2011 by John Wiley & Sons, Ltd. ISBN: 978-0-470-71411-9


2

Heterocycles in Life and Society

properties very similar to those of aliphatic secondary amines, such as diethylamine, and
1,2,5,6-tetrahydropyridine resembles both a secondary amine and an alkene.

H2C
H2C

H2
C
C
H2

CH2
CH2

H2C
H2C

Cyclohexane

H2C
H2C

H2
C
N
H

CH2
CH2

Piperidine

H
C
C
H2

HC
HC

Cyclohexene

C

H

CH
CH

HC
HC

Benzene

H2C
H2C

CH
CH2

H
C

H
C
N
H

H
C
N

CH
CH

Pyridine

CH
CH2

1,2,5,6-Tetrahydropyridine

..

..

N
H
A

N
B

H

Figure 1.1 The relationship between cyclic hydrocarbons and heterocycles and the two chair conformations of piperidine.

An interesting feature of heterocycloalkanes and heterocycloalkenes is the possibility of their
existence in several geometrically distinct nonplanar forms which can quite easily (without bond
cleavage) equilibrate with each other. Such forms are called conformations. For instance, piperidine
exists mainly in a pair of chair conformations in which the internal angle between any pair of
bonds is close to tetrahedral (109◦ 28 ) to minimize steric strain. In these two chair conformations
(Figure 1.1), the N—H proton is in either the equatorial (A) or axial (B) position, the first being
slightly preferred.

By contrast, the heteroaromatic compounds, as the most important group of heterocycles, possess
highly specific features. Historically, the name ‘aromatic’ for derivatives of benzene, naphthalene
and their numerous analogues came from their characteristic physical and chemical properties.
Aromatic compounds differ from other groups in possessing thermodynamic stability. Thus, they
are resistant to heating and tend to be oxidized and reduced with difficulty. On treatment with
electrophilic, nucleophilic and radical agents, they mainly undergo substitution of hydrogen atoms
rather than the addition reactions to multiple bonds which are typical for ethylene and other
alkenes. Such behavior results from the peculiar electronic configuration of the aromatic ring. We
consider in the next section the structure of benzene and some parent heteroaromatic molecules.

1.2

Building Heterocycles From Benzene

Each carbon atom in the benzene molecule formally participates in bond formation with its four
atomic orbitals, each occupied by one electron. Three of these orbitals are hybridized and are called
sp 2 -orbitals. Their axes lie in the same plane and are directed from each other at an angle of 120◦ .
These atomic orbitals overlap similar orbitals of adjacent carbon atoms or the s-orbitals of hydrogen


Molecular Rings Studded With Jewels

3

atoms, thereby forming the ring framework of six carbon–carbon bonds and six carbon–hydrogen
bonds (Figure 1.2a). The molecular orbitals and bonds thus formed are called σ-orbitals and
σ-bonds, respectively. The fourth electron of the carbon atom is located in an atomic p-orbital,
which is dumbbell shaped and has an axis perpendicular to the ring plane (Figure 1.2b). If the
p-orbitals merely overlapped in pairs, the benzene molecule would possess the cyclohexatriene
structure with three single and three conjugated double bonds, as reflected in the classic representation of benzene – the Kekul´e structure (Figure 1.2c). However, in reality, the benzene

ring is a regular hexagon, which indicates equal overlap of each p-orbital with its two neighboring
p-orbitals, resulting in the formation of a completely delocalized π-electron cloud (Figure 1.2d, e).

(a)

(b)

(c)

0

0

↓↑

↓↑
↓↑

(d)

(e)

(f)

Figure 1.2 The electronic structure of the benzene molecule: (a) framework of σ-bonds, (b) p-orbital
orientation, (c) overlap of p-orbitals forming localized π-bonds (view from above), (d) overlap of p-orbitals
forming delocalized π-bonds, (e) representation of the benzene ring reflecting the equivalence of all
carbon-carbon bonds and the equal distribution of π-electrons, (f) energy levels of molecular π-orbitals
showing electron occupation of the three orbitals of lower energy.

Thus, in the benzene molecule as well as in the molecules of other aromatic compounds, we
observe a new type of carbon–carbon bond called ‘aromatic’, which is intermediate in length
˚
between a single and a double bond. Standard aromatic C—C bond lengths are close to 1.40 A,
˚ in ethane and 1.34 A
˚ in ethylene.
whereas the C—C distance is 1.54 A
The high stability of the benzene molecule is explained by the energetic picture available from
quantum mechanics. Benzene has six molecular π-orbitals. Three of these π-orbitals (bonding
orbitals) lie below the nonbonding energy level and are occupied by six electrons with a large
energy stabilization. The remaining three are above the nonbonding level (antibonding orbitals).
Occupation of the bonding orbitals leads to the formation of strong bonds and stabilizes the
molecule as a whole. Incomplete occupation of bonding orbitals, and especially the occupation
of antibonding orbitals, results in considerable destabilization. Figure 1.2f shows that all three
bonding orbitals in benzene are completely occupied. Hence, it is often said that benzene has a
stable aromatic π-electron sextet, a concept that can be compared in its importance to the inert
octet cloud of neon or the F− anion.
In addition to the π-electron sextet, stable aromatic arrangements can also be formed by 2, 10,
14, 18 or 22 π-electrons. Such molecules contain cyclic sets of delocalized π-electrons. For
example, the aromatic molecule naphthalene possesses 10 π-electrons. The number of electrons


4

Heterocycles in Life and Society

required for a stable aromatic configuration can be calculated by the 4n + 2 ‘H¨uckel rule’, where
n = 0, 1, 2, 3 and so on, which was suggested by the German scientist H¨uckel in the early 1930s.1
The electronic configuration of the pyridine molecule is very similar to that of benzene
(Figure 1.3a). Both compounds contain an aromatic π-electron sextet. However, the presence

of the nitrogen heteroatom in the case of pyridine results in significant changes in the cyclic
molecular structure. First, the nitrogen atom has five valence electrons in the outer shell, in
contrast with the carbon atom which has only four. Two take part in the formation of the
skeletal carbon–nitrogen σ-bonds, and a third electron is utilized in the aromatic π-cloud. The
two remaining electrons are unshared, their sp 2 -orbitals lying in the plane of the ring. Owing
to the availability of this unshared pair of electrons, the pyridine molecule undergoes many
additional reactions over and above those which are characteristic of benzene or other aromatic
hydrocarbons. Second, nitrogen is a more electronegative element than carbon and therefore
attracts electron density. The distribution of the π-electron cloud in the pyridine ring is thus
distorted (see Chapter 2).

N

..

..

(a)

N

H

(b)

Figure 1.3 The orientation of π-electron orbitals and unshared electron pairs in (a) pyridine and (b)
pyrrole (C—H bonds are omitted).

Heterocyclic compounds include examples containing many other heteroatoms such as phosphorus, oxygen, sulfur and so on. By substitution of a ring carbon atom we may formally transform
benzene into phosphabenzene or pyrylium and thiapyrylium cations (Figure 1.4). Note that a sixmembered ring which includes oxygen or another group VI element can only be aromatic if the

heteroatom bears a formal positive charge (+1). Such cationic rings exist only in association with
counterions like ClO4 − or BF4 − . Just like the nitrogen atom in pyridine, the phosphorus, oxygen
and sulfur atoms donate one π-electron to the aromatic electron cloud. Such heteroatoms are often
called ‘pyridine-like’.

X
Phosphabenzene (X = P)
Pyrylium (X = O+)
Thiapyrylium (X = S+)

..
X
Pyrrole (X = NH)
Furan (X = O)
Thiophene (X = S)

Figure 1.4 Examples of heterocycles with pyridine-like and pyrrole-like heteroatoms.

Formally, pentagonal aromatic heterocycles can also be derived from benzene by a heteroatom
taking the place of one complete CH CH group. Two electrons of the heteroatom p-orbital must
1 For monocyclic fully conjugated compounds, the H¨uckel rule stops working with 26 and larger π-electron systems (n ≥ 6).
This is explained by a strong increase of inter-electron repulsion that outweighs the gain of aromatic stabilization.


Molecular Rings Studded With Jewels

5

now be involved in the π-system in order to obtain an aromatic sextet (Figure 1.3b). This type of
heteroatom is called ‘pyrrole-like’ in contrast to the ‘pyridine-like’ nitrogen which donates only

one electron to the sextet. The corresponding five-membered heterocycles containing nitrogen,
oxygen or sulfur atoms are named pyrrole, furan and thiophene, respectively (Figure 1.4). One
more difference between a pyridine-like heteroatom and a pyrrole-like heteroatom is obvious: the
first participates with one double bond in the Kekul´e structure, while the second is involved with
single bonds only.
A heterocycle can contain several heteroatoms. Pyridazine, pyrimidine, pyrazine and 1,3,5triazine are heterocyclic compounds with a single ring but two or three identical heteroatoms
(Figure 1.5a). Together with pyridine and many other analogues they form the family of azines.
N

N

(a)

N

N
Pyridazine

N

N
1,3,5-Triazine

N
Pyrazine

N
Pyrimidine

N

N
(b)

N

N

N

N

X

X

N
H

Pyrazole (X = NH)
Isoxazole (X = O)
Isothiazole (X = S)

Imidazole (X = NH)
Oxazole (X = O)
Thiazole (X = S)

Tetrazole

Figure 1.5 Heterocycles of (a) the azine class and (b) the azole class.

Five-membered heterocyclic compounds containing both pyridine-like and pyrrole-like nitrogen
or other heteroatoms are called azoles. Pyrazole, imidazole and their oxygen and sulfur analogues
belong to the azole series (Figure 1.5b).
Two or more rings are encountered in many heterocyclic compounds. The rings may be connected to each other by a single bond (as in the case of 2,2 -bipyridyl) or may be fused as shown
in Figure 1.6 to form condensed systems. For example, two fused rings exist in quinoline, pteridine, indole and benzimidazole and three fused rings in acridine. In some cases a heteroatom may
belong simultaneously to two (e.g., indolizine) or even three rings. Such a heteroatom is denoted
a ‘bridgehead’ atom.
N

N
N

N

N

N

N

N

H
2,2′-Bipyridyl

Quinoline

Pteridine

Indole

N
N

N

N

H
Benzimidazole

Acridine

Indolizine

Figure 1.6 Examples of bi- and polycyclic heterocycles.


6

1.3

Heterocycles in Life and Society

Some More Kinds of Heterocycles

The comparison of heterocycles with jewel-studded rings is most appropriate for five- and
six-membered systems which are frequently natural products and which have become commonplace in many research laboratories. However, polymembered cycles or macrocycles have
recently drawn much attention. They resemble not so much finger-rings but rather molecular

bracelets or bangles. For example, aza[18]annulene is an 18-membered analogue of pyridine, and
aza[17]annulene is a 17-membered analogue of pyrrole (Figure 1.7a). We focus our attention on
macrocycles in subsequent chapters, especially Chapter 10.

(a)

N

N
H

Aza[18]annulene

Aza[17]annulene

H
N

N

Azafullerenyl radical

Azahydro[60]fullerene

(b)

Fullerene
H−
+ B +
HN

NH
(c)
HB
−

+N
H

BH
−

N

N

N

N

N
N

N
CH3

Pri2N

B

Pri2N

B

NPri2

B
B
NPri2

Borazine

N

CH3

N N

1-(p-Dimethylaminophenyl)pentazole

1,2,3,4-Tetrakis(diisopropylamino)
cyclotetraborane

N
N

Hexazine

Figure 1.7 Examples of (a) macroheterocycles, (b) azafullerenes and (c) rings without cyclic carbon
atoms.

Another recently arisen area is the chemistry of heterofullerenes – compounds in which one
or more cage carbon atoms are substituted by heteroatoms. The most stable among them are


Molecular Rings Studded With Jewels

7

azafullerenes. The valence rules determine that, at the introduction of one nitrogen atom into the
fullerene molecule C60 , the free radical specie C59 N• should be produced. Its stabilization can
be achieved either via dimerization into 2,2 -biaza[60]fullerene (C59 N)2 or by means of hydrogen
atom addition leading to green azahydro[60]fullerene C59 NH (Figure 1.7b). Carbon nanotubes
containing nitrogen or boron heteroaatoms are also known.
How many heteroatoms may be included in one ring? As many as one can imagine. A ring
may, in principle, be completely constructed from noncarbon atoms (Figure 1.7c). Borazine,
a well known example of such a compound, was designated ‘inorganic benzene’ because
of its high stability. 1-(p-Dimethylaminophenyl)pentazole and blue-colored 1,2,3,4-tetrakis
(diisopropylamino)cyclotetraborane contain five- and four-membered heterocycles composed
only of nitrogen or boron atoms. The curiosity of many chemists has long been excited by a
theoretical substance named ‘hexazabenzene’ or ‘hexazine’. Numerous attempts to prepare this
compound have so far ended in failure, supposedly because of its great instability and tendency
to decompose to give nitrogen: N6 → 3N2 .
Of course, the examples given above by far do not cover all of the heterocyclic systems possible.
In the following chapters we will become acquainted with many new ones.


8

1.4

Heterocycles in Life and Society

Problems

1. How many chair conformations are possible for unsubstituted piperidine? How many for a
1,4-disubstituted piperidine? Draw their structures.
2. The boat conformation for saturated six-membered rings is energetically unfavorable. Account
for this fact. Design the structure of a substituted piperidine in which the boat conformation is
fixed.
3. Phosphacyclohexane (phosphorinane) exists almost completely in a chair conformation with the
P—H bond axial. Discuss possible reasons for the stabilization of this conformation compared
with the analogous piperidine conformation.
4. Indicate which of the heterocycles listed below can be formally regarded as aromatic. Explain
your choices.
H
B

CH3

B
H

CH3
O

B
CH3

(a)

(b)

(c)

(d)
N

Si H

N
+

N

N
N

N
(e)

(f)

N
N

(g)

5. Historically, the first synthetic homocyclic aromatic system not containing carbon atoms was
the golden-orange salt P5 − Na+ . Draw its structure and explain the following facts: (i) the salt
is stable only in tetrahydrofuran solution in the presence of 18-crown-6 (see Section 10.1.1),

(ii) all phosphorus atoms in the anion P5 − in solution are equivalent.
6. Draw all of the possible isomeric imidazopyridines, that is, the heterocycles which consist of
fused pyridine and imidazole nuclei.
7. What is the orientation of the nitrogen lone pair of electrons in aza[18]annulene (Figure 1.7)?
Is any alternative orientation possible? Discuss the orientation of the N—H bond in
aza[17]annulene.
8. The relative stability (aromaticity) of five-membered heterocycles is changed in the following
sequence: thiophene> pyrrole> furan. How this can be explained?
9. To avoid the formation of a free radical by placing one nitrogen atom into fullerene, one can
simultaneously introduce into the molecule two heteroatoms. Draw the simplest structures of
such a type.

1.5

Suggested Reading

1. Joule, J. A., Heterocyclic Chemistry, 4th edn, Wiley-Blackwell, Chichester, 2000.
2. Gilchrist, T. L., Heterocyclic Chemistry, 3rd edn, Pearson Education Press, London, 1997.


Molecular Rings Studded With Jewels

9

3. Katritzky, A. R., Ramsden, C. A., Joule, J. A. and Zhdankin, V. V., Handbook of Heterocyclic
Chemistry, 3rd edn, Elsevier, 2010.
4. Katritzky, A. R., Ramsden C., Scriven E. and Taylor, R. (eds), Comprehensive Heterocyclic
Chemistry III , vols 1–15, Elsevier, New York, 2008.
5. Katritzky, A. R., Rees, C. W. and Scriven E. (eds), Comprehensive Heterocyclic Chemistry II ,
vols 1–12, Pergamon Press, Oxford, 1995.

6. Katritzky, A. R. and Rees, C. W. (eds), Comprehensive Heterocyclic Chemistry, vols 1–8,
Pergamon Press, Oxford, 1984.
7. Elguero, J., Marzin, C., Katritzky, A. R. and Linda, P. The tautomerism of heterocycles, in
Advances in Heterocyclic Chemistry, Suppl. 1 , Academic Press, New York, 1976.
8. Pozharskii, A. F., Theoretical Basis of Heterocyclic Chemistry (in Russian), Khimia, Moscow,
1985.
9. Katritzky, A. R. (ed.) Special issue on heterocyclic chemistry, Chem. Rev ., 2004, 104 (5).


2
Why Nature Prefers Heterocycles
Ties subtle, full of power exist
Between the shape and flavor of a flower.
So is a brilliant unseen, until comes hour
To facet it from diamond mist.
V. Bryusov

All biological processes are chemical in nature. Such fundamental manifestations of life as the provision of energy, transmission of nerve impulses, sight, metabolism and the transfer of hereditary
information are all based on chemical reactions involving the participation of many heterocyclic
compounds. Why does nature utilize heterocycles? To answer this question we first describe the
basic physical and physicochemical properties of the fundamental heterocyclic types.

2.1

Reactions for all Tastes

Heterocycles are involved in an extraordinarily wide range of reaction types. Depending on the pH
of the medium, they may form anions or cations. Some interact readily with electrophilic reagents,
others with nucleophiles and yet others with both. Some are easily oxidized, but resist reduction,
while others can be readily hydrogenated but are stable toward the action of oxidizing agents.

Certain amphoteric heterocyclic systems simultaneously demonstrate all of the above-mentioned
properties. The ability of many heterocycles to produce stable complexes with metal ions has
great biochemical significance. Such versatile reactivity is linked to the electronic distributions in
heterocyclic molecules. Let us consider pyridine.
We have already seen that the nitrogen atom in pyridine induces π-electron withdrawal from
the carbon atoms. As a result of this electronic shift, the carbon atoms in the ortho and para
positions (relative to the nitrogen atom) acquire a partial positive charge (Figure 2.1). Thus, a
π-electron deficit on the carbon skeleton is characteristic of all heterocycles containing pyridinelike heteroatoms. Such heterocycles are called π-deficient.

Heterocycles in Life and Society: An Introduction to Heterocyclic Chemistry, Biochemistry and Applications,
Second Edition. Alexander F. Pozharskii, Anatoly T. Soldatenkov and Alan R. Katritzky.
© 2011 John Wiley & Sons, Ltd. Published 2011 by John Wiley & Sons, Ltd. ISBN: 978-0-470-71411-9


12

Heterocycles in Life and Society
+0.050
−0.004
+0.077

−0.004
N
−0.195

+0.077

−0.105
−0.035

−0.105

N −0.287
+0.035

−0.068
−0.037

−0.035
N +0.28
H

N +0.298
H

Figure 2.1 The π-electron charges in pyridine, pyrrole and imidazole.

A unique feature of π-deficient heterocycles is their facile interaction with negatively charged
nucleophilic reagents. As a typical example, the reaction of pyridine with sodamide gives
2-aminopyridine in good yield:
1) Na+NH2−,
toluene, 110°C

+ H2↑ + NaOH

2) H2O

N

N

NH2

Substitution of the hydrogen atom under the action of positively charged (electrophilic) agents
proceeds with difficulty or does not occur at all in π-deficient heterocycles. However, electrophiles
add readily to the pyridine nitrogen owing to its unshared pair of electrons. Pyridine thus forms
pyridinium and N -alkylpyridinium salts with acids and alkyl halides, respectively, and a zwitterionic addition compound or Lewis salt with BF3 :
d+ d−
CH3 l
+
N
CH3

l−

HCl
+
N

N

H
BF3

N-Methylpyridinium iodide

Cl−

Pyridinium chloride

+
N
BF3−
Addition compound or
Lewis salt

Pyridine and other heterocycles containing a pyridine-like nitrogen atom behave as bases in
these and similar reactions (see Section 2.2).
The introduction of electron-accepting groups into an organic compound lowers the energy of all
molecular orbitals. Hence, such compounds donate electrons with difficulty and are thus poorly oxidized. By contrast, their ability to accept additional electrons enables such compounds to be readily


Why Nature Prefers Heterocycles

13

reduced. Pyridine-like heteroatoms are electron acceptors, and hence π-deficient heterocycles are
reduced with ease. This is found to be the case, especially in relation to compounds which have
a positively charged heteroatom, like salts of pyrylium, pyridinium and so on. For example,
1-benzyl-3-carbamoylpyridinium chloride is reduced by sodium dithionite to the corresponding
1,4-dihydropyridine derivative:
H
CONH2
+
N

H
CONH2

Na2S2O4

H2O

Cl−

N

CH2C6H5

CH2C6H5

We shall see elsewhere (Sections 4.2.1 and 5.2) that nature uses this apparently simple reaction
to drive a great many biologically important processes.
Quite a different situation is encountered in the case of pyrrole, furan and thiophene. Since
the heteroatoms of these compounds each contribute two electrons to the π-aromatic ensemble,
the cyclic system of five atoms formally has six π-electrons. As a result, in spite of the higher
intrinsic electronegativity of the heteroatom, all of the carbon atoms possess excess negative charge
(Figure 2.1). Such compounds are named π-excessive heterocycles. Reactions with nucleophiles
agents are not common but they readily interact with electrophiles. Thus, pyrrole is almost instantly
halogenated even under very mild conditions to give the tetrahalogenopyrrole, and these reactions
cannot be stopped at the monosubstitution stage:
Br

Br2
C2H5OH, 0°C
N
H

Br

Br

N
H

Br

Two-electron donation to the aromatic system by the pyrrole-like heteroatom imparts a partial
positive charge to the heteroatom (Figure 2.1). In the case of pyrrole and related NH-heterocycles,
the N—H bond reactivity increases. N-Anions, which are readily alkylated, acylated and arylated,
are thus formed under the action of bases. Such reactions are commonly used for the synthesis
of various N-derivatives (note that a nonionized NH group does not, as a rule, undergo these
conversions):
RX

KOH
N
H

N
−

−KX
K+

N
R

The molecular orbitals in π-excessive heterocycles are of high energy, and consequently
these compounds are reduced with difficulty but are readily oxidized. Compounds with
both pyridine-like and pyrrole-like heteroatoms, as expected, can show both π-deficient and

π-excessive properties with one or the other dominant. Thus, imidazole contains two carbon
atoms with a partial negative and a third with a partial positive π-charge (Figure 2.1). Its high
reactivity towards halogenation is attributed to the dominant π-excessive character of the neutral
molecule and especially of the imidazole anion.


14

Heterocycles in Life and Society

2.2

Heterocycles as Acids and Bases

In the preceding section we noted the capability of nitrogen heterocycles to behave as acids or
bases, the acidic properties being inherent to heterocyclic compounds containing a pyrrole-like
NH group, whereas the basic properties are characteristic for those with pyridine-like nitrogen.
We describe this in more detail because acid–base properties play a vital role not only in general
reactivity but in many biochemical processes as well.
The acid dissociation constant (Ka ) is universally used as the quantitative measure of acidity.
Dissociation constants are obtained by application of the law of mass action to the acid–base
equilibrium:
H−A
H+ + A−
The dissociation constant Ka is equal to the anion concentration multiplied by the proton concentration, divided by the concentration of the nondissociated acid:
Ka = [A− ][H+ ]/[HA]

(2.1)

In practice, following the analogous use of pH, it is more convenient to use the negative

logarithm of Ka , the so-called acidity index pKa :
pKa = − log Ka = − log[A− ] − log[H+ ] + log[HA]
as the value of −log[H+ ] = pH, then:
pKa = log{[HA]/[A− ]} + pH

(2.2)

It is clear from Equation (2.2) that the value of the pKa is equal to the value of the pH when the
nondissociated acid (HA) content and the anion (A− ) content are equal, that is, when the degree
of dissociation is 50%.
We see that the stronger the acid, the greater the numerator and, consequently, the larger the Ka
value; a larger Ka value corresponds to a smaller pKa . Vice versa, in a series of compounds, the pKa
increases as the acidity decreases. It should be emphasized that pKa values, which are essentially
acid ionization constants, are also employed for the measurement of basicity. As a consequence of
the reversibility of the dissociation process, any acid which donates its proton is thus converted to
the conjugate base; similarly, a base which accepts a proton becomes the conjugate acid. Stronger
acids obviously correspond to weaker conjugate bases and vice versa. Thus, for bases, the order
of the pKa changes in the opposite sense: the larger the pKa of the conjugate acid, the stronger
the base, and the weaker bases have correspondingly lower pKa values.
The acid dissociations of pyrrole and imidazole (Figure 2.2a) are used as an example. The
corresponding pKa values are 17.5 and 14.2, respectively.1 As pKa is a logarithmic scale, pyrrole
is a weaker acid than imidazole by a factor of 103.3 (i.e., by a factor of 2000). This also indicates
that the pyrrole anion is a stronger base than the imidazole anion by the same factor.
Whereas both pyrrole and imidazole are very weak acids, some heterocycles have pKa values
close to those of conventional acids. Tetrazole (Figure 1.5) has a pKa of 4.89, almost equal to that
of acetic acid (pKa 4.76).
Under ordinary conditions a neutral pyrrole-like nitrogen is unlikely to add a proton because of
the tendency to preserve the aromaticity of the heterocycle. In contrast, the lone electron pair of
1 Standardized conditions must be used for the determination of ionization constants as the latter depend on solvent and
temperature. The pKa values given here were determined in aqueous solutions at 20 ◦ C.

Why Nature Prefers Heterocycles

15

a pyridine nitrogen does not participate in the formation of the aromatic sextet and readily adds
a proton to form a heteroaromatic cation. Thus, pyridine has a pKa of 5.23. This value formally
reflects the acidity of the pyridinium ion (Figure 2.2b), but is more often used to assess the basicity
of pyridine. It can be seen that the proton of the pyridinium cation is 12 orders of magnitude more
acidic than the NH of pyrrole. This is readily explained by the facile loss of a proton from the
positively charged nitrogen atom in the pyridinium cation.
Z

Z
(a)
N

+

N

H+

Pyrrole: Z = CH
Imidazole: Z = N

H

+

(b)

H+

N

+
N
H
+ H
N

N
(c)
N

+

H+

H

H

H
N

N
+

N

N+

N

H

H

H

Figure 2.2 Acid–base equilibria for pyrrole (a), imidazole (a, c) and pyridine (b).

Obviously, heterocycles such as imidazole have amphoteric properties: imidazole is both an
NH acid and a strong neutral base with a pKa of 6.95. The imidazole ring system is frequently
encountered in proteins (see Section 4.1) and is one of the strongest of all bases found in biological
systems. The imidazole unit, therefore, plays an active role in proton transfer processes and the
various catalytic events accompanying them. The enhanced basicity of imidazole is due to electron
donation from the pyrrole nitrogen, thus favoring proton addition. The stabilized imidazolium ion
can be represented by two equivalent resonance structures in which the positive charge is isolated
on one nitrogen atom in the first representation and on the other in the second, or by an average
structure with delocalized charge (Figure 2.2c). Section 10.1.5 contains some additional information
on the basicity of nitrogen heterocycles.

2.3

Heterocycles and Metals

It is well known that minute quantities of different metals are necessary for the normal development
of all living organisms. In addition to the widespread sodium, potassium, magnesium, calcium, iron
and zinc, the group of ‘essential metals’ also includes more exotic members such as molybdenum,
cobalt, chromium and others. Metals exist in organisms in the form of cations linked with various
basic ligands by coordination bonds. The basic functionality may involve the amino, hydroxy or
thiol groups of amino acids as well as nitrogen heterocycles (azines, azoles). The ability to form
stable metallic complexes seems to be ‘preprogrammed’ into the structure of the heterocycles.
The fixed and outwardly directed unshared pair of electrons of a pyridine nitrogen atom is
available for coordination with practically all metal ions. Thus, pyridine gives complexes of various