A SELF-STUDY GUIDE TO THE

PRINCIPLES OF ORGANIC CHEMISTRY

 A SELF-STUDY GUIDE TO THE
PRINCIPLES OF ORGANIC CHEMISTRY
Key Concepts, Reaction Mechanisms,
and Practice Questions for the Beginner

JIBEN ROY

Universal-Publishers
Boca Raton
 A Self-Study Guide to the Principles of Organic Chemistry:
Key Concepts, Reaction Mechanisms, and Practice Questions for the Beginner

Copyright © 2013 Jiben Roy

All rights reserved.
No part of this book may be reproduced or transmitted in any form or by any means, electronic
or mechanical, including photocopying, recording, or by any information storage and retrieval
system, without written permission from the publisher

Universal-Publishers
Boca Raton, Florida
USA • 2013

ISBN-10: 1-61233-261-7
ISBN-13: 978-1-61233-261-1

www.universal-publishers.com

Cover image © Can Stock Photo Inc. / Marcopolo

Library of Congress Cataloging-in-Publication Data

Roy, Jiben.
A self-study guide to the principles of organic chemistry : key concepts, reaction mechanisms, and
practice questions for the beginner / Jiben Roy.
pages cm
ISBN-13: 978-1-61233-261-1 (paperback : alkaline paper)
ISBN-10: 1-61233-261-7 (paperback : alkaline paper)
1. Chemistry, Organic--Study and teaching. 2. Chemistry, Organic--Problems, exercises, etc. I. Title.
QD256.R68 2013
547--dc23
2013019602
 To 4 W & 1M
Wrishija
Wrijoya
Writtika
Rita
&
Manish

 
  
Contents

Preface .................................................................................................................................................... vii

About the Author................................................................................................................................... ix

Chapter 1: Introduction to Organic Chemistry ................................................................................. 1

Chapter 2: Atoms, Bonding, Orbitals, Hybridization, Polarity and Electronegativity .............. 11
Chapter 3: Resonance ......................................................................................................................... 25
Chapter 4: Hydrocarbons and Functional Groups ......................................................................... 37
Chapter 5: Stereochemistry: Part I .................................................................................................... 47
Chapter 6: Stereochemistry: Part II................................................................................................... 53
Chapter 7: Organic Reactions ............................................................................................................63
Chapter 8: Reactions of Alkenes ....................................................................................................... 73
Chapter 9: Nucleophilic Substitution and Elimination Reaction ................................................. 83
Chapter 10: Organic Analysis Using Spectroscopic Techniques .................................................. 99
Chapter 11: Aromaticity - Benzene and its Reactions ..................................................................113
Chapter 12: Alcohols and Phenols ..................................................................................................131
Chapter 13: Carbonyl Compounds..................................................................................................141
Chapter 14: Malonic Ester and Acetoacetic Ester Synthesis .......................................................157
Chapter 15: Organic Base: Amines .................................................................................................163
Chapter 16: Biomolecules – Carbohydrates ...................................................................................171
Chapter 17: Biomolecules - Amino Acids and Proteins ...............................................................181
Chapter 18: Biomolecules – Lipids: Fats and Oils, Steroids ........................................................189
Chapter 19: Biomolecules – Nucleic Acid, DNA and RNA .......................................................195
Chapter 20: Industrial Organic Polymers.......................................................................................201
Chapter 21: Synthetic Approach to Organic Compounds...........................................................205
Chapter 22: Miscellaneous Important Aspects of Organic Chemistry ......................................215
Chapter 23: Sample Exam in Organic Chemistry .........................................................................225
Chapter 24: Appendix-1: Answer to Additional Questions and Sample Exam .......................231

v
 To the students taking the course of
Organic Chemistry

 
  

This book, A Self-Study Guide to the Principles of Organic Chemistry: Key Concepts, Reaction Mechanisms, and
Practice Questions for the Beginner is written in plain and simple language and it is formatted as a self-study
guidebook for the students. For instructors, it is a handbook dealing with all the concepts necessary to
understand organic chemistry. It may not be a comprehensive organic chemistry textbook, and cer-
tainly it is not going to replace the existing comprehensive organic chemistry textbook, but it has all
the elements to build the student’s skill and foundation in understanding as well as learning organic
chemistry. This book can be considered as the 21st century ‘Rosetta Stone,’ used to study this foreign
language, organic chemistry. By studying this book, students struggling with organic chemistry will be
able to grasp the key concepts easily.
Some students taking organic chemistry are very scared of the class, but this central science sub-
ject is a requirement for chemistry majors, biology majors or many more related majors. It is intended
for both 2 year and 4 year colleges.
Starting with a definition, the book explains atoms, electronic configuration, bonding, hydroca-
bons, polar reaction mechanism, stereochemistry, reaction varieties, organic spectroscopy, aromaticity
and aromatic reactions, essential organic functionalities and their reactions, biomolecules, organic
polymers, and a synthetic approach to organic compounds. It emphasizes visual conception through
the use of structural drawings and mechanisms, with less narrative so that the student can better visu-
alize the principles of organic chemistry. Students will discover how logical organic chemistry is, and
they will certainly need less memorization practicing with pen and paper. Each chapter ends with
frequently asked questions and answers, followed by additional practice problems with the answers at
the back. The questions and answers section of each chapter is an integral part of the formulae for
understanding organic chemistry. Almost all the most essential concepts in organic chemistry are
introduced in a systematic manner so that the students find them logical, easier, and challenging as
well.
I am really happy to have found a person like Jeff Young who has built up a publishing company
based on publishing unique books at a lower cost while taking care of a worthy manuscript from A to
Z. I am thankful to Jeff for selecting and taking care of my book in publication and distribution to the
students around the world. I am also indebted to the production editor of my book, Christie Mayer,
and cover designer, Shereen Siddiqui, who each did an excellent job on the book.
I am thankful to my organic chemistry students, especially the class of Fall 2012, who have used
part of the manuscript and found it effective in their understanding. I am grateful to my colleagues
Dr. Dionne Fortenberry, Dr. Ghanshyam Heda, and friends and well-wishers for their encourage-
ment. Finally, I would appreciate hearing from the students and instructors about the book and its
improvement for the future.

________________
Jiben Roy
Columbus, Mississippi
[email protected]

vii
  

Dr. Jiben Roy is a professor of chemistry in the Department of Sciences and Mathematics, Mississippi
University for Women. He earned his Ph.D. in organic chemistry from the University of Saskatche-
wan, Canada in 1983, and went on to complete his post-doctoral fellowship at the Hawaii Natural
Energy Institute, University of Hawaii at Manoa 1984-1985. Dr. Roy has established an impressive
track record in teaching and research, while also working in the pharmaceutical industry with bulk
drugs and formulations, both in the United States and abroad. His publications include An Introduction
to Pharmaceutical Sciences: Production, Chemistry, Techniques & Technology (2011), Organic Chemistry (in Benga-
li) (1979), over four dozen other publications, and a co-edited special issue of the journal Current Me-
dicinal Chemistry.

ix
    
1 Introduction to Organic Chemistry

1.1 6.5 Definition of Organic Chemistry

Sugar, gasoline, peanut butter, plastics, aspirin, paper, milk, cotton, wood, meat, apples, spinach, beer
and most of the substances important to life and life styles have one thing common: they all contain
the element CARBON (C). Carbon is such a unique and important element that an entire branch of
chemistry studying carbon and its compounds is known as organic chemistry. Organic chemistry is
thus the study of the chemistry of carbon containing compounds. Several millions of such com-
pounds are currently known. A more appropriate definition of organic chemistry is: The chemistry
of hydrocarbons (compounds of carbon and hydrogen only) and the derivatives of hydrocar-
bons, (compounds containing C, H, and O, N, S, P, halogens etc). In some organic com-
pounds, the metals such as Na, K, Ca and many others can be found. These compounds are called
organo-metallic compounds.
However, there are some exceptions: carbonates (CO3-2), bicarbonates (HCO3-1), cyanides (CN-1)
of metals, CS2 and a few gases such as CO, CO2, HCN etc., are not considered organic compounds.
Thus, they are treated in Inorganic Chemistry. However, the compounds containing carbon and hy-
drogen, i.e. hydrocarbons, are always considered organic compounds. This is the foundation of organ-
ic chemistry. The derivatives of hydrocarbon, i.e., the compounds derived from hydrocarbon by re-
placing one or more atoms of hydrogen, form the vast majority of organic compounds (Figure 1.1).

1
2 A Self-Study Guide to the Principles of Organic Chemistry

Figure 1.1 Hydrocarbon, methane and its derivatives

The Periodic Table contains more than one hundred elements; however, organic chemistry deals
mostly with only certain elements. The partial Periodic Table is shown below (Figure 1.2), where
the elements involved in organic compounds are shown in black.
Period

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18

1 1 2
H He
2 3 4 5 6 7 8 9 10
Li Be B C N O F Ne
3 11 12 13 14 15 16 17 18
Na Mg Al Si P S Cl  Ar
4 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 Kr
K Ca Sc Ti V Cr Mn Fe Co Ni Cu Zn Ga Ge As Se Br 36
5 53 54
I Xe

Figure 1.2 The Partial Periodic Table where the elements mostly involved in Organic Compounds are
shown in black shade. Group 1= Alkali metals (except H); Group 2= Alkaline earth metals; Group
17=Halogens; Group 18=Inert or noble gas

1.2 6.5   Electron Configuration of the Elements Commonly Involved

in Organic Compounds
It is thus very important to know the properties of these elements involved in organic compounds
(Table 1.1). The electronic configuration of these elements would help to understand the structure of
organic compounds. Most of the elements are non-metal, except Li, Na, Mg, K, and Ca, which are the
metals that form organo-metallic compounds, as previously mentioned. Information on isotopes of
these elements involved in organic compounds is also included. Isotopes have same atomic number
(number of protons) but a different mass number (number of neutrons). Examples: Hydrogen with
 Introduction to Organic Chemistry 3
Mass number 1(no neutron) has two more isotopes, deuterium with mass number 2 (1 neutron) and
tritium with mass number 3 (2 neutrons). Similarly carbon has 12C which is almost 99% available nat-
urally with two other isotopes, 13C and 14C.

Table 1.1 Fact Sheet of most common elements in Organic Compounds

Name of Group Block At. No. Physical Electron Configuration Isotopes

element (Period) (At. State
(Symbol) mass)
Hydrogen 1 s 1 Gas(H2) 1s1 1H,2H, 3H

(H) (1) (1)

Lithium 1 s 3 Solid 1s22s1 or [He]2s1 7Li, 6Li

(Li) (2) (7)

Carbon 14 p 6 Solid 1s22s22p2 or 1s22s22px12py12pz0 12C,13C, 14C

(C) (2) (12) or [He]2s22p2

Nitrogen 15 p 7 Gas(N2) 1s22s22p3 or 1s22s22px12py12pz1 14N

(N) (2) (14) or [He]2s22p3

Oxygen 16 p 8 Gas(O2) 1s22s22p4 or 1s22s22px22py12pz1 16O, 18O

(O) (2) (16) or [He]2s22p4

Fluorine 17 p 9 Gas(F2) 1s22s22p5 or 1s22s22px22py22pz1 19F

(F) (2) (19) or [He]2s22p5

Sodium 1 s 11 Solid 1s22s22p63s1 or 23Na

(Na) (3) (23) [Ne]3s1

Magnesium 2 s 12 Solid 1s22s22p63s2 or 24Mg,25Mg,

(Mg) (3) (24) [Ne]3s2 26Mg

Phosphorus 15 p 15 Solid 1s22s22p63s23p3 or 31P

(P) (3) (31) [Ne] 3s23p3

Sulfur 16 p 16 Solid 1s22s22p63s23p4 or 32S

(S) (3) (32) [Ne] 3s23p4

Chlorine 17 p 17 Gas 1s22s22p63s23p5 or 35Cl, 37Cl

(Cl) (3) (35.5) (Cl2) [Ne] 3s23p5

Potassium 1 s 19 Solid 1s22s22p63s23p64s1 or 39K

(K) (4) (39) [Ar]4s1

Calcium 2 s 20 Solid 1s22s22p63s23p64s2 or 40Ca

(Ca) (4) (40) [Ar]4s2

Bromine 17 p 35 Liquid 1s22s22p63s23p63d104s24p5 or 79Br, 81Br

(Br) (4) (80) (Br2) [Ar] 3d104s24p5

Iodine 17 p 53 Solid 1s22s22p63s23p63d104s24p6- 127I

(I) (5) (127) (I2) 4d105s25p5 or [Kr] 4d105s25p5

The building up (Aufbau Principle) of electron configuration with the increase of atomic number
(similar increase in number of electrons) depends on the energy levels of orbitals. Orbital energy lev-
els are shown in Figure 1.3. You can see 1s orbital has the lowest energy, then 2s, followed by 2p
orbitals. The 2p orbitals consist of 3 degenerate orbitals.
4 A Self-Study Guide to the Principles of Organic Chemistry

Figure 1.3 The Orbital Energy Diagram

1.3 Occurrences,
              Importance and Hazards of Organic Compounds

Organic chemistry is a versatile discipline of sciences. The human body is made up of organic com-
pounds. We synthesize organic compounds and we also eat organic compounds. We have industry
based on organic compounds. A few examples are shown below:

[a] Living organisms: Living organisms ingest organic compounds and convert it into almost all of
the compounds necessary for life.

Food DNA, amino acids, polypeptides, proteins, enzymes, fats, glycosides, etc.

O
NH2 H
N O
N H2N N
N H HO
O HN H
H O
O N N O
O HN O
-
O P O H HO OH
O HO N HO H
- H H N H
O H
H H O O H
OH H
DNA Nucleotide with adenine base Polypeptide Glycoside
 Introduction to Organic Chemistry 5
[b] Industrial Organic Compounds: Carbon containing substances are converted into useful prod-
ucts.

Coal, oil, natural gas plastics, fibres, dyes, detergents,

solvents, chemical building blocks

[c] Fine Chemical Industry: Complex molecules are synthesized from simpler ones.

Simpler carbon compounds Pharmaceuticals, agrochemicals, Cosmetics

[d] Environmental hazards: Industrial processes have produced a number of environmentally dan-
gerous organic compounds, including Freon (destroys ozone layer), pesticides, (DDT), dioxin, PCB,
and abused drugs.

[e] Branches of Science Based on Organic Chemistry: Biotechnology, microbiology, biochemis-

try, pharmacy, medical sciences, agriculture.

At a glance, these applications of organic chemistry (organic compounds) can be seen in Figure 1.4.
6 A Self-Study Guide to the Principles of Organic Chemistry

Figure 1.4 Application of organic chemistry

1.4 Why are there Millions of Organic Compounds

(Carbon Containing Compounds)?
There are number of characteristics of carbon and carbon compounds which can explain the for-
mation of millions of organic compounds. The number of organic compounds is increasing every day.

[1] Carbon forms 4 covalent bonds with other non-metal atoms and these 4 bonds can be formed in
different ways.
 Introduction to Organic Chemistry 7
[2] Carbon also forms organometallic compounds containing carbon – metal bonds.

 
C M (Highly polar, covalent Organocmetallic compounds)
H3C - Li : Methyl Litium R - MgX : Alkyl magnesium halide (Grignard reagent)
(CH3) 2 Cu Li : Lithium dialkyl Copper (Gilman reagent)

[3] Carbon to carbon bond formations, also known as catenation, can be formed in many different
ways: straight, branching or alicyclic and aromatic.

C C C C C C

C
Straight Chain Branched alicyclic aromatic

[4] Isomerism – the same molecular formula but in a different structure can lead to many different
compounds, for example pentane can have two more isomers. Similarly, decane can have a total of 75
isomers. Hydrocarbon derivatives also rearrange to produce isomers, such as n-butanol and isobuta-
nol.

OH

OH

n-pentane iso-pentane neo-pentane n-butanol iso-butanol

[5] Functional group derivatives of carbon – using just 2 carbon chains could lead to many deriva-
tives. A few derivatives are shown below.
8 A Self-Study Guide to the Principles of Organic Chemistry
[6] Organic acids form ionic compounds with metals to form salts.

[7] Formation of heterocyclic compounds- if there is 1 or 2 atoms other than carbon in the ring, het-
erocyclic compounds are formed.

1.5 Frequently Asked Questions & Answers

1] Write an electron configuration of ground and excited state of carbon atom.

Answer

Carbon has 6 electrons, which has the following electron configuration:

(Ground state) C(6) = 1s22s22p2 or 1s22s22px12py12pz0 or 1s22s22px12py1 or [He]2s22p2
(Excited state) C*(6) = 1s22s12px12py12pz1 or [He]2s12px12py12pz1

2] What would be electron configuration of Na+ and Cl-?

Answer

Sodium (Na) has 11 electrons and in Na+ ion, there is 1 less electron than Na. However, Cl- will have
1 more electron compared to Cl (17 electrons).

Na(11) = 1s22s22p63s1 or [Ne]3s1

Na+(10) = 1s22s22p6 or [Ne]

Cl(17) = 1s22s22p63s23p5 or [Ne] 3s23p5

Cl-(18) = 1s22s22p63s23p6 or [Ar]
 Introduction to Organic Chemistry 9
3] Name an organic compound containing phosphorous or sulfur.

Answer

Most important example of P-containing organic compound is DNA (Deoxyribonucleic acid), which
is a polymer and its monomer is nucleotide. Similar to alcohol, there is thiol, such as CH3CH2-SH.

4] [Multiple choice question] Which one is not an organic compound?

(a) sucrose (b) splenda (c) cooking gas (d) baking soda (e) PVC

Answer

Correct is (d) baking soda (NaHCO3)

1.6 Additional Practice Questions (Answers at the back)

5] Draw all the possible isomers of hexane.

6] What are the isotopes of chlorine? Include their natural abundance.

7] How many electrons 2p, 3p and 3d orbitals can accommodate?

   
Atoms, Bonding, Orbitals, Hybridization,
2 Polarity, and Electronegativity

2.1 6.5 Atoms

An atom is the smallest fundamental unit of an element. It is made up of nucleus surrounded by

orbiting electron(s). The proton and neutron in the nucleus at the center of atom are fixed; however,
electron(s) is(are) always in motion. The positively charged nucleus is attracted by the moving nega-
tively charged electron.

Nucleus : consists of proton (positively charged) and neuton (neutral).

Proton Hydrogen atom is only exception where there is only proton & no neutron.
Neutron
Negatively charged electrons

Figure 2.1 Atomic Structure

Charge Mass number (6 protons + 6 neutrons)

Mass number
(superscript on the lef t) b c (superscript on the right) 12
d (subscript on the right) 6
(subscript on the lef t) a Atomic number (Number of protons)
Atomic number Number of atoms
Elemental symbol

11
12 A Self-Study Guide to the Principles of Organic Chemistry

2.2 Bond
              Formation and Arrangement of Electrons
When one atom comes close to another atom, a bond is formed. A pair of electrons through sharing
makes a bond (covalent bonding). Or the bond may be formed by the transfer of electrons making
positive and negatively charged ions (ionic). The question is electrons are negatively charged, so when
they come closer, there should be repulsion. In that case, how is a bond formed?
In fact, positively charged nucleus of one atom is also attracted by the negatively electron of the
other atom and vice versa (Figure 2.2).

+ +
+ +

e e

H . H . ..
H H
Hydrogen atoms Hydrogen molecule
Figure 2.2 Formation of bond between two hydrogen atoms

To understand bonding, we need to refresh our memory with the arrangement of electrons around
the nucleus of an atom. The electrons are distributed in different orbitals (sub-energy levels), which
are housed in different orbit or shells (energy levels). The arrangement of electrons around the nucle-
us is summarized in Figure 2.3. It is important to remember that it is only valence electrons that can
participate in bonding. In addition, during the formation of covalent bonds in organic compounds,
the unpaired electrons make bonds.

Figure 2.3 Arrangement of electrons around the nucleus

 Atoms, Bonding, Orbitals, Hybridization, Polarity, and Electronegativity 13

2.3 Valance Electrons

Valence electrons are those that inhabit the outermost shells, energy levels, or highest principal quan-
tum number. These electrons participate in making bonds. On the other hand, the electrons in the
inner shells, which do not participate in making bonds, are called core electrons. From the electron
configuration, both core and valence electrons can be determined. The number of valence electrons
and number of possible bonds are shown in Table 2.1.

Table 2.1 Determination of valence electrons based on electron configuration

Name of At. Electron Configuration Block No. Number Number
element No (Valence electrons are in of Core of Valence of possible
(Symbol) bold) electrons electrons bonds
Hydrogen 1 1s1 s 0 1 1
(H)
Carbon 6 1s22s22p2 or p 2 4 4
(C) 1s22s22px12py12pz0
or [He]2s22p2
Nitrogen 7 1s22s22p3 or p 2 5 3
(N) 1s22s22px12py12pz1
or [He]2s22p3
Oxygen 8 1s22s22p4 or p 2 6 2
(O) 1s22s22px22py12pz1
or [He]2s22p4
Fluorine 9 1s22s22p5 or p 2 7 1
(F) 1s22s22px22py22pz1
or [He]2s22p5
Sodium 11 1s22s22p63s1 or s 10 1 1
(Na) [Ne]3s1
Phosphorus 15 1s22s22p63s23p3 or p 10 5 3 or 5
(P) [Ne] 3s23p3
Sulfur 16 1s22s22p63s23p4 or p 10 6 2
(S) [Ne] 3s23p4
Chlorine 17 1s22s22p63s23p5 or p 10 7 1
(Cl) [Ne] 3s23p5
Potassium 19 1s22s22p63s23p64s1 or s 18 1 1
(K) [Ar]4s1
Calcium 20 1s22s22p63s23p64s2 or s 18 2 2
(Ca) [Ar]4s2
Bromine 35 1s22s22p63s23p63d104s24p5 or p 28 7 1
(Br) [Ar] 3d104s24p5
Iodine 53 1s22s22p63s23p63d104s24p64d10 p 46 7 1
(I) 5s25p5 or [Kr] 4d105s25p5