231-232 ORGANIC

CHEMISTRY
TABLE OF CONTENTS
The element carbon has unique properties making it a foundation for very large and wonderfully intricate molecules. The properties and
function of the more than 50 million unique substances the human race understands, most of which are organic compounds, can be
understood by exploring the composition, connectivity, shape, and sense of carbon-based molecules. Organic Chemistry is a challenging
and valuable discussion transferable to both the UC and CSU systems.

1: STRUCTURE AND BONDING

This chapter provides a review of material covered in a standard freshman general-chemistry course through a discussion of the
following topics: the differences between organic and inorganic chemistry. the shapes and significance of atomic orbitals. electron
configurations. ionic and covalent bonding. molecular orbital theory. hybridization. the structure and geometry of the compounds
methane, ethane, ethylene and acetylene.

1.1: Prelude to Structure and Bonding

1.2: Atomic Structure - The Nucleus
1.3: Atomic Structure - Orbitals
1.4: Atomic Structure - Electron Configurations
1.5: Development of Chemical Bonding Theory
1.6: The Nature of Chemical Bonds - Valence Bond Theory
1.7: sp³ Hybrid Orbitals and the Structure of Methane
1.8: sp³ Hybrid Orbitals and the Structure of Ethane
1.9: sp² Hybrid Orbitals and the Structure of Ethylene
1.10: sp Hybrid Orbitals and the Structure of Acetylene
1.11: Hybridization of Nitrogen, Oxygen, Phosphorus and Sulfur
1.12: The Nature of Chemical Bonds: Molecular Orbital Theory
1.13: Drawing Chemical Structures
1.14: Structure and Bonding (Summary)

2: POLAR COVALENT BONDS; ACIDS AND BASES

This chapter provides a review of the more advanced material covered in a standard introductory chemistry course through a discussion
of the following topics: the drawing and interpretation of organic chemical structures. the use of ball-and-stick molecular models. the
concept of formal charge. the use of electronegativities to determine bond polarity, and the application of this knowledge to determining
whether a given molecule possesses a dipole moment. the Brønsted-Lowry and Lewis definition

2.1: Polar Covalent Bonds - Electronegativity

2.2: Polar Covalent Bonds - Dipole Moments
2.3: Formal Charges
2.4: Resonance
2.5: Rules for Resonance Forms
2.6: Drawing Resonance Forms
2.7: Acids and Bases - The Brønsted-Lowry Definition
2.8: Acid and Base Strength
2.9: Predicting Acid-Base Reactions from pKa Values
2.10: Organic Acids and Organic Bases
2.11: Acids and Bases - The Lewis Definition
2.12: Molecular Models
2.13: Polar Covalent Bonds; Acids and Bases (Summary)

3: ORGANIC COMPOUNDS: ALKANES AND THEIR STEREOCHEMISTRY

This chapter begins with an introduction to the concept of the functional group, a concept that facilitates the systematic study of organic
chemistry. Next, we introduce the fundamentals of organic nomenclature (i.e., the naming of organic chemicals) through examination of
the alkane family of compounds. We then discuss, briefly, the occurrence and properties of alkanes, and end with a description of cis-
trans isomerism in cycloalkanes.

3.1: Chapter Objectives

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3.2: Functional Groups
3.3: Alkanes and Alkane Isomers
3.4: Alkyl Groups
3.5: Naming Alkanes
3.6: Properties of Alkanes
3.7: Conformations of Ethane
3.8: Conformations of Other Alkanes
3.9: Gasoline - A Deeper Look

4: ORGANIC COMPOUNDS: CYCLOALKANES AND THEIR

STEREOCHEMISTRY
4.1: Chapter Objectives
4.2: Naming Cycloalkanes
4.3: Cis-Trans Isomerism in Cycloalkanes
4.4: Stability of Cycloalkanes - Ring Strain
4.5: Conformations of Cycloalkanes
4.6: Conformations of Cyclohexane
4.7: Axial and Equatiorial Bonds in Cyclohexane
4.8: Conformations of Monosubstituted Cyclohexanes
4.9: Conformations of Disubstituted Cyclohexanes
4.10: Conformations of Polycyclic Molecules

5: STEREOCHEMISTRY AT TETRAHEDRAL CENTRES

5.1: Chapter Objectives
5.2: Enantiomers and the Tetrahedral Carbon
5.3: The Reason for Handedness in Molecules - Chirality
5.4: Optical Activity
5.5: Pasteur's Discovery of Enantiomers
5.6: Sequence Rules for Specifying Configuration
5.7: Diastereomers
5.8: Meso Compounds
5.9: Racemic Mixtures and the Resolution of Enantiomers
5.10: A Review of Isomerism
5.11: Chirality at Nitrogen, Phosphorus, and Sulfur
5.12: Prochirality
5.13: Chirality in Nature and Chiral Environments
5.14: 5:3 Enantiomers
5.15: Meso Compounds

6: AN OVERVIEW OF ORGANIC REACTIONS

6.1: Chapter Objectives
6.2: Kinds of Organic Reactions
6.3: How Organic Reactions Occur - Mechanisms
6.4: Radical Reactions
6.5: Polar Reactions
6.6: An Example of a Polar Reaction - Addition of HBr to Ethylene
6.7: Using Curved Arrows in Polar Reaction Mechanisms
6.8: Describing a Reaction - Equilibria, Rates, and Energy Changes
6.9: Describing a Reaction - Bond Dissociation Energies
6.10: Describing a Reaction - Energy Diagrams and Transition States
6.11: Describing a Reaction: Intermediates
6.12: A Comparison between Biological Reactions and Laboratory Reactions

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7: ALKENES - STRUCTURE AND REACTIVITY
This, the first of two chapters devoted to the chemistry of alkenes, describes how certain alkenes occur naturally, then shows the
industrial importance of ethylene and propylene (the simplest members of the alkene family). The electronic structure of alkenes is
reviewed, and their nomenclature discussed in detail.

7.1: Chapter Objectives

7.2: Introduction to Alkenes
7.3: Industrial Preparation and Use of Alkenes
7.4: Calculating Degree of Unsaturation
7.5: Naming Alkenes
7.6: Cis-Trans Isomerism in Alkenes
7.7: Sequence Rules - The E,Z Designation
7.8: Stability of Alkenes
7.9: Electrophilic Addition Reactions of Alkenes
7.10: Orientation of Electrophilic Additions - Markovnikov's Rule
7.11: Carbocation Structure and Stability
7.12: The Hammond Postulate
7.13: Evidence for the Mechanism of Electrophilic Additions - Carbocation Rearrangements

8: ALKENES: REACTIONS AND SYNTHESIS

8.1: Chapter Objectives
8.2: Preparation of Alkenes - A Preview of Elimination Reactions
8.3: Halogenation of Alkenes - Addition of X₂
8.4: Halohydrins from Alkenes - Addition of HOX
8.5: Hydration of Alkenes - Addition of H₂O by Oxymercuration
8.6: Hydration of Alkenes - Addition of H₂O by Hydroboration
8.7: Reduction of Alkenes - Hydrogenation
8.8: Oxidation of Alkenes - Epoxidation and Hydroxylation
8.9: Oxidation of Alkenes - Cleavage to Carbonyl Compounds
8.10: Addition of Carbenes to Alkenes - Cyclopropane Synthesis
8.11: Radical Additions to Alkenes - Chain-Growth Polymers
8.12: Biological Additions of Radicals to Alkenes
8.13: Stereochemistry of Reactions - Addition of H₂O to an Achiral Alkene
8.14: Stereochemistry of Reactions - Addition of H₂O to a Chiral Alkene

9: ALKYNES - AN INTRODUCTION TO ORGANIC SYNTHESIS

9.1: Chapter Objectives
9.2: Naming Alkynes
9.3: Preparation of Alkynes - Elimination Reactions of Dihalides
9.4: Reactions of Alkynes - Addition of HX and X₂
9.5: Hydration of Alkynes
9.6: Reduction of Alkynes
9.7: Oxidative Cleavage of Alkynes
9.8: Alkyne Acidity - Formation of Acetylide Anions
9.9: Alkylation of Acetylide Anions
9.10: An Introduction to Organic Synthesis

10: ORGANOHALIDES
10.1: Chapter Objectives
10.2: Introduction to Organohalides
10.3: Names and Properties of Alkyl Halides
10.4: Preparing Alkyl Halides from Alkanes - Radical Halogenation
10.5: Preparing Alkyl Halides from Alkenes - Allylic Bromination
10.6: Stability of the Allyl Radical - Resonance Revisited
10.7: Preparing Alkyl Halides from Alcohols
10.8: Reactions of Alkyl Halides - Grignard Reagents

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10.9: Organometallic Coupling Reactions
10.10: Oxidation and Reduction in Organic Chemistry

11: REACTIONS OF ALKYL HALIDES: NUCLEOPHILIC SUBSTITUTIONS AND

ELIMINATIONS
11.1: Chapter Objectives
11.2: Introduction
11.3: The Discovery of Nucleophilic Substitution Reactions
11.4: The Sₙ2 Reaction
11.5: Characteristics of the Sₙ2 Reaction
11.6: The Sₙ1 Reaction
11.7: Characteristics of the Sₙ1 Reaction
11.8: Biological Substitution Reactions
11.9: Elimination Reactions: Zaitsev's Rule
11.10: The E2 Reaction and the Deuterium Isotope Effect
11.11: The E2 Reaction and Cyclohexane Conformation
11.12: A Summary of Reactivity - S N 1, S N 2, E1, E1cB, and E2
11.12: The E1 and E1cB Reactions
11.13: Biological Elimination Reactions

12: STRUCTURE DETERMINATION: MASS SPECTROMETRY AND INFRARED

SPECTROSCOPY
12.1: Chapter Objectives
12.2: Introduction
12.3: Mass Spectrometry of Small Molecules: Magnetic-Sector Instruments
12.4: Interpreting Mass Spectra
12.5: Mass Spectrometry of Some Common Functional Groups
12.6: Mass Spectrometry in Biological: Time-of-flight (TOF) Instruments
12.7: Spectroscopy and the Electromagnetic Spectrum
12.8: Infrared Spectroscopy
12.9: Interpreting Infrared Spectra
12.10: Infrared Spectra of Some Common Functional Groups

13: STRUCTURE DETERMINATION - NUCLEAR MAGNETIC RESONANCE

SPECTROSCOPY
In Chapter 12, you learned how an organic chemist could use two spectroscopic techniques, mass spectroscopy and infrared
spectroscopy, to assist in determining the structure of an unknown compound. This chapter introduces a third technique, nuclear
magnetic resonance (NMR). The two most common forms of NMR spectroscopy, ¹H NMR and ¹³C NMR, will be discussed, the former
in much more detail than the latter.

13.1: Chapter Objectives

13.2: Nuclear Magnetic Resonance Spectroscopy
13.3: The Nature of NMR Absorptions
13.4: Chemical Shifts
13.5: ¹³C NMR Spectroscopy - Signal Averaging and FT-NMR
13.6: Characteristics of ¹³C NMR Spectroscopy
13.7: DEPT ¹³C NMR Spectroscopy
13.8: Uses of ¹³C NMR Spectroscopy
13.9: ¹H NMR Spectroscopy and Proton Equivalence
13.10: Chemical Shifts in ¹H NMR Spectroscopy
13.11: Integration of ¹H NMR Absorptions: Proton Counting
13.12: Integration of ¹H NMR Absorptions: Proton Counting
13.13: Spin-Spin Splitting in ¹H NMR Spectra
13.14: More Complex Spin-Spin Splitting Patterns
13.15: Uses of ¹H NMR Spectroscopy

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14: CONJUGATED COMPOUNDS AND ULTRAVIOLET SPECTROSCOPY
In this chapter, you will focus your attention on compounds that contain two or more such bonds. In particular you will study the
properties of those compounds that contain two carbon-carbon double bonds which are separated by one carbon-carbon single bond.
These compounds are called “conjugated dienes.” To understand the properties exhibited by conjugated dienes, you must first examine
their bonding in terms of the molecular orbital theory.

14.1: Chapter Objectives

14.2: Introduction
14.3: Stability of Conjugated Dienes - Molecular Orbital Theory
14.4: Electrophilic Additions to Conjugated Dienes - Allylic Carbocations
14.5: Kinetic vs. Thermodynamic Control of Reactions
14.6: The Diels-Alder Cycloaddition Reaction
14.7: Characteristics of the Diels-Alder Reaction
14.8: Diene Polymers - Natural and Synthetic Rubbers
14.9: Structure Determination in Conjugated Systems - Ultraviolet Spectroscopy
14.10: Interpreting Ultraviolet Spectra - The Effect of Conjugation
14.11: Conjugation, Color, and the Chemistry of Vision

15: BENZENE AND AROMATICITY

15.1: Chapter Objectives
15.2: Introduction
15.3: Sources and Names of Aromatic Compounds
15.4: Structure and Stability of Benzene
15.5: Aromaticity and the Hückel 4n 2 Rule
15.6: Aromatic Ions
15.7: Aromatic Heterocycles - Pyridine and Pyrrole
15.8: Polycyclic Aromatic Compounds
15.9: Spectroscopy of Aromatic Compounds

16: CHEMISTRY OF BENZENE - ELECTROPHILIC AROMATIC SUBSTITUTION

16.1: Chapter Objectives
16.2: Introduction
16.3: Electrophilic Aromatic Substitution Reactions - Bromination
16.4: Other Aromatic Substitutions
16.5: Alkylation and Acylation of Aromatic Rings - The Friedel-Crafts Reaction
16.6: Substituent Effects in Substituted Aromatic Rings
16.7: An Explanation of Substituent Effects
16.8: Trisubstituted Benzenes - Additivity of Effects
16.9: Nucleophilic Aromatic Substitution
16.10: Benzyne
16.11: Oxidation of Aromatic Compounds
16.12: Reduction of Aromatic Compounds
16.13: Synthesis of Polysubstituted Benzenes

17: ALCOHOLS AND PHENOLS

In this unit, we examine the chemistry of the alcohol family of compounds. Alcohols can undergo a wide variety of reactions, and
because of this reactivity and because they can be prepared in a number of different ways, alcohols occupy an important position in
organic chemistry. The discussion begins with an outline of the nomenclature of alcohols and phenols. We review the physical
properties of these compounds, and discuss methods used to obtain the lower members on an industrial scale.

17.1: Chapter Objectives

17.2: 17.0 Introduction
17.3: 17.1 Naming Alcohols and Phenols
17.4: 17.2 Properties of Alcohols and Phenols
17.5: A Review
17.6: Reduction

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17.7: Grignard Reagents
17.8: 17.6 Reactions of Alcohols
17.9: 17.7 Oxidation of Alcohols
17.10: 17.8 Protection of Alcohols
17.11: 17.9 Phenols and Their Uses
17.12: 17.10 Reactions of Phenols
17.13: 17.11 Spectroscopy of Alcohols and Phenols

18: ETHERS AND EPOXIDES; THIOLS AND SULFIDES

We shall begin in a very traditional manner, with a discussion of the nomenclature of ethers. We will then describe how ethers may be
prepared in the laboratory, and discuss the relative inertness of these compounds. A discussion of the chemistry of cyclic ethers follows,
with particular emphasis on the preparation and reactions of epoxides—cyclic ethers containing a three‑membered ring. We will then
introduce crown ethers.

18.1: Chapter Objectives

18.2: Introduction
18.3: Names and Properties of Ethers
18.4: Synthesis of Ethers
18.5: Reactions of Ethers - Acidic Cleavage
18.6: Reactions of Ethers - Claisen Rearrangement
18.7: Cyclic Ethers - Epoxides
18.8: Reactions of Epoxides - Ring-opening
18.9: Crown Ethers
18.10: Thiols and Sulfides
18.11: Spectroscopy of Ethers
18.12: Affix - A Preview of Carbonyl Compounds

19: ALDEHYDES AND KETONES: NUCLEOPHILIC ADDITION REACTIONS

Nucleophilic addition reactions were described in general terms in Unit 18. In Unit 19, we take a more detailed look at these reactions
as we make a comprehensive study of the chemistry of aldehydes and ketones. Aldehydes and ketones are discussed together because
their chemistry is very similar. However, as you work through the unit, be sure to look for specific instances where the chemistry of
these two classes of compounds differs.

19.1: Chapter Objectives

19.2: 19.1 Naming Aldehydes and Ketones
19.3: 19.2 Preparing Aldehydes and Ketones
19.4: 19.3 Oxidation of Aldehydes and Ketones
19.5: 19.4 Nucleophilic Addition Reactions of Aldehydes and Ketones
19.6: Hydration
19.7: Cyanohydrin Formation
19.8: Alcohol Formation
19.9: Imine and Enamine Formation
19.10: 19.9 Nucleophilic Addition of Hydrazin - The Wolff-Kishner Reaction
19.11: Acetal Formation
19.12: The Wittig Reaction
19.13: 19.12 Biological Reductions
19.14: 19.13 Conjugate Nucleophilic Addition to α, β-unsaturated Aldehydes and Ketones
19.15: 19.14 Spectroscopy of Aldehydes and Ketones

20: CARBOXYLIC ACIDS AND NITRILES

20.1: Chapter Objectives
20.2: 20.0 Introduction
20.3: 20.1 Naming Carboxylic Acids and Nitriles
20.4: 20.2 Structure and Properties of Carboxylic Acids
20.5: 20.3 Biological Acids and the Henderson-Hasselbalch Equation
20.6: 20.4 Substituent Effects on Acidity
20.7: 20.5 Preparing Carboxylic Acids

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20.8: An Overview
20.9: 20.7 Chemistry of Nitriles
20.10: 20.8 Spectroscopy of Carboxylic Acids and Nitriles

21: CARBOXYLIC ACID DERIVATIVES: NUCLEOPHILIC ACYL SUBSTITUTION

REACTIONS
21.1: Chapter Objectives
21.2: 21.0 Introduction
21.3: 21.1 Naming Carboxylic Acid Derivatives
21.4: 21.2 Nucleophilic Acyl Substitution Reactions
21.5: 21.3 Nucleophilic Acyl Substitution Reactions of Carboxylic Acids
21.6: 21.4 Chemistry of Acid Halides
21.7: 21.5 Chemistry of Acid Anhydrides
21.8: 21.6 Chemistry of Esters
21.9: 21.7 Chemistry of Amides
21.10: Biological Carboxylic Acid Derivatives
21.11: Step-Growth Polymers
21.12: 21.10 Spectroscopy of Carboxylic Acid Derivatives

22: CARBONYL ALPHA-SUBSTITUTION REACTIONS

Alpha-substitution reactions are the third major type of reaction that you will study in your investigation of the chemistry of carbonyl
compounds. As you will see, these reactions proceed through the formation of the enol form of the carbonyl compound. After a brief
review of keto-enol tautomerism, we begin our discussion of alpha-substitution reactions by looking at the methods used to introduce a
halogen atom into a carbonyl-containing compound—reactions.

22.1: Chapter Objectives

22.2: 22.0 Introduction
22.3: 22.1 Keto-Enol Tautomerism
22.4: The Mechanism of Alpha-Substitution Reactions
22.5: 22.3 Alpha Halogenation of Aldehydes and Ketones
22.6: 22.4 Alpha Bromination of Carboxylic Acids
22.7: Enolate Ion Formation
22.8: 22.6 Reactivity of Enolate Ions
22.9: 22.7 Alkylation of Enolate Ions

23: CARBONYL CONDENSATION REACTIONS

Carbonyl condensation reactions take place between two carbonyl containing reactants, one of which must possess an alpha-hydrogen
atom. The first step of the reaction involves the removal of an alpha-hydrogen atom by a base. In the second step, the enolate anion that
results from this removal attacks the carbonyl-carbon of the second reacting molecule. In the final step , a proton is transferred to the
tetrahedral intermediate formed in the second step, but may subsequently be dehydrated.

23.1: Chapter Objectives

23.2: 23.1 Carbonyl Condensations - The Aldol Reaction
23.3: 23.2 Carbonyl Condensations versus Alpha Substitutions
23.4: 23.3 Dehydration of Aldol Products - Synthesis of Enones
23.5: 23.4 Using Aldol Reactions in Synthesis
23.6: 23.5 Mixed Aldol Reactions
23.7: 23.6 Intramolecular Aldol Reactions
23.8: 23.7 The Claisen Condensation Reaction
23.9: Mixed Claisen Condensations
23.10: 23.9 Intramolecular Claisen Condensations - The Dieckmann Cyclization
23.11: 23.10 Conjugate Carbonyl Additions - The Michael Reaction
23.12: 23.11 Carbonyl Condensations with Enamines - The Stork Reaction
23.13: 23.12 The Robinson Annulation Reaction
23.14: 23.13 Some Biological Carbonyl Condensation Reactions

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24: AMINES AND HETEROCYCLES
Amines are the first nitrogen-containing compounds that we study in detail in this course.We begin the unit with an explanation of the
differences in structure among primary, secondary and tertiary amines. We explain the nomenclature of aliphatic and anylamines, and
examine the structure and bonding of these compounds, relating these features to their physical properties and basicity.

24.1: Chapter Objectives

24.2: 24.1 Naming Amines
24.3: Structure and Properties of Amines
24.4: Basicity of Amines
24.5: 24.4 Basicity of Arylamines
24.6: 24.5 Biological Amines and the Henderson-Hasselbalch Equation
24.7: 24.6 Synthesis of Amines
24.8: 24.7 Reactions of Amines
24.9: 24.8 Reactions of Arylamines
24.10: 24.9 Heterocyclic Amines
24.11: 24.10 Spectroscopy of Amines

25: BIOMOLECULES: CARBOHYDRATES

25.1: Chapter Objectives
25.2: 25.0 Introduction
25.3: 25.1 Classification of Carbohydrates
25.4: Fischer Projections
25.5: 25.3 D, L Sugars
25.6: 25.4 Configurations of Aldoses
25.7: Anomers
25.8: Reactions of Monosaccharides
25.9: 25.7 The Eight Essential Monosaccharides
25.10: 25.8 Disaccharides
25.11: 25.9 Polysaccharides and Their Synthesis
25.12: 25.10 Other Important Carbohydrates
25.13: 25.11 Cell-Surface Carbohydrates and Influenza Viruses

26: BIOMOLECULES: AMINO ACIDS, PEPTIDES, AND PROTEINS

Amino acids are important biochemicals, as they are the building blocks from which proteins and polypeptides are assembled.We begin
this unit with an examination of some of the fundamental chemistry of amino acids: their structures, stereochemistry and synthesis. We
then discuss the nature of peptides and of the peptide bond, and present the complex issue of determining the order in which the various
amino acid residues occur in a given peptide.

26.1: Chapter Objectives

26.2: 26.0 Introduction
26.3: 26.1 Structures of Amino Acids
26.4: 26.2 Amino Acids, the Henderson-Hasselbalch Equation, and Isoelectric Points
26.5: 26.3 Synthesis of Amino Acids
26.6: 26.4 Peptides and Proteins
26.7: 26.5 Amino Acid Analysis of Peptides
26.8: The Edman Degradation
26.9: 26.7 Peptide Synthesis
26.10: The Merrifield Solid-Phase Technique
26.11: 26.9 Protein Structure
26.12: 26.10 Enzymes and Coenzymes
26.13: 26.11 How do Enzymes Work? Citrate Synthase

27: BIOMOLECULES - LIPIDS

Lipids are naturally occurring organic compounds that can be extracted from cells and tissues using nonpolar solvents. Although many
lipids have complex structures, their chemistry can often be understood quite readily by applying the basic concepts you have studied in
previous units. We begin the unit with a study of fats and oils, and explain the different origins of these structurally similar substances.

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27.1: Chapter Objectives
27.2: 27.0 Introduction to Lipids
27.3: 27.1 Waxes, Fats, and Oils
27.4: 27.2 Soap
27.5: 27.3 Phospholipids
27.6: Prostaglandins and Other Eicosanoids
27.7: Terpenoids
27.8: 27.6 Steroids
27.9: Biosynthesis of Steroids

28: BIOMOLECULES - NUCLEIC ACIDS

28.1: Chapter 28 Objectives
28.2: Nucleotides and Nucleic Acids
28.3: Base Pairing in DNA - The Watson-Crick Model
28.4: Replication of DNA
28.5: Transcription of DNA
28.6: Translation of RNA - Protein Biosynthesis
28.7: DNA Sequencing
28.8: DNA Synthesis
28.9: The Polymerase Chain Reaction

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1: STRUCTURE AND BONDING
This chapter provides a review of material covered in a standard freshman general-chemistry course through a discussion of the
following topics: the differences between organic and inorganic chemistry. the shapes and significance of atomic orbitals. electron
configurations. ionic and covalent bonding. molecular orbital theory. hybridization. the structure and geometry of the compounds
methane, ethane, ethylene and acetylene.

1.1: PRELUDE TO STRUCTURE AND BONDING

Organic compounds contain carbon atoms bonded hydrogen and other carbon atoms. Organic chemistry studies the properties and
reactions of organic compounds.

1.2: ATOMIC STRUCTURE - THE NUCLEUS

Atoms are comprised of protons, neutrons and electrons. Protons and neutrons are found in the nucleus of the atom, while electrons are
found in the electron cloud around the nucleus. The relative electrical charge of a proton is +1, a neutron has no charge, and an
electron’s relative charge is -1. The number of protons in an atom’s nucleus is called the atomic number, Z. The mass number, A, is the
sum of the number of protons and the number of neutrons in a nucleus.

1.3: ATOMIC STRUCTURE - ORBITALS

An atomic orbital is the probability description of where an electron can be found. The four basic types of orbitals are designated as s, p,
d, and f.

1.4: ATOMIC STRUCTURE - ELECTRON CONFIGURATIONS

The order in which electrons are placed in atomic orbitals is called the electron configuration and is governed by the aufbau principle.
Electrons in the outermost shell of an atom are called valence electrons. The number of valence electrons in any atom is related to its
position in the periodic table. Elements in the same periodic group have the same number of valence electrons.

1.5: DEVELOPMENT OF CHEMICAL BONDING THEORY

Lewis Dot Symbols are a way of indicating the number of valence electrons in an atom. They are useful for predicting the number and
types of covalent bonds within organic molecules. The molecular shape of molecules is predicted by Valence Shell Electron Pair
Repulsion (VSEPR) theory. The shapes of common organic molecules are based on tetrahedral, trigonal planar or linear arrangements of
electron groups.

1.6: THE NATURE OF CHEMICAL BONDS - VALENCE BOND THEORY

Covalent bonds form as valence electrons are shared between two atoms. Lewis Structures and structural formulas are common ways of
showing the covalent bonding in organic molecules. Formal charge describes the changes in the number of valence electrons as an atom
becomes bonded into a molecule. If the atom has a net loss of valence electrons it will have a positive formal charge. If the atom has a
net gain of valence electrons it will have a negative formal charge.

1.7: SP³ HYBRID ORBITALS AND THE STRUCTURE OF METHANE

The four identical C-H single bonds in methane form as the result of sigma bond overlap between the sp3 hybrid orbitals of carbon and
the s orbital of each hydrogen.

1.8: SP³ HYBRID ORBITALS AND THE STRUCTURE OF ETHANE

The C-C bond in ethane forms as the result of sigma bond overlap between a sp³ hybrid orbital on each carbon. and the s orbital of each
hydrogen. The six identical C-H single bonds in form as the result of sigma bond overlap between the sp³ hybrid orbitals of carbon and
the s orbital of each hydrogen.

1.9: SP² HYBRID ORBITALS AND THE STRUCTURE OF ETHYLENE

The C=C bond in ethylene forms as the result of both a sigma bond overlap between a sp2 hybrid orbital on each carbon and a pi bond
overlap of a p orbital on each carbon

1.10: SP HYBRID ORBITALS AND THE STRUCTURE OF ACETYLENE

The carbon-carbon triple bond in acetylene forms as the result of one sigma bond overlap between a sp hybrid orbital on each carbon
and two pi bond overlaps of p orbitals on each carbon.

1.11: HYBRIDIZATION OF NITROGEN, OXYGEN, PHOSPHORUS AND SULFUR

The atomic orbitals of nitrogen, oxygen, phosphorus and sulfur can hybridize in the same way as those of carbon.

1.12: THE NATURE OF CHEMICAL BONDS: MOLECULAR ORBITAL THEORY

Molecular Orbital theory (MO) is a more advanced bonding model than Valence Bond Theory, in which two atomic orbitals overlap to
form two molecular orbitals – a bonding MO and an anti-bonding MO.

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1.13: DRAWING CHEMICAL STRUCTURES
Kekulé Formulas or structural formulas display the atoms of the molecule in the order they are bonded. Condensed structural formulas
show the order of atoms like a structural formula but are written in a single line to save space. Skeleton formulas or Shorthand formulas
or line-angle formulas are used to write carbon and hydrogen atoms more efficiently by replacing the letters with lines. Isomers have the
same molecular formula, but different structural formulas

1.14: STRUCTURE AND BONDING (SUMMARY)

TOC.2 Updated 7/14/2019

1.1: PRELUDE TO STRUCTURE AND BONDING
OBJECTIVES
After completing this section, you should be able to
1. Define organic chemistry as the study of carbon-containing compounds.
2. Explain why the results of the experiments carried out by Chevreul and Wöhler contributed to the demise of the “vital force”
theory.

KEY TERMS
Make certain that you can define, and use in context, the key term below.
organic chemistry

All living things on earth are formed mostly of carbon compounds. The prevalence of carbon compounds in living things has led to the
epithet “carbon-based” life. The truth is we know of no other kind of life. Early chemists regarded substances isolated from organisms
(plants and animals) as a different type of matter that could not be synthesized artificially, and these substances were thus known as
organic compounds. The widespread belief called vitalism held that organic compounds were formed by a vital force present only in
living organisms. The German chemist Friedrich Wöhler was one of the early chemists to refute this aspect of vitalism, when, in 1828,
he reported the synthesis of urea, a component of many body fluids, from nonliving materials. Since then, it has been recognized that
organic molecules obey the same natural laws as inorganic substances, and the category of organic compounds has evolved to include
both natural and synthetic compounds that contain carbon. Some carbon-containing compounds are not classified as organic, for
example, carbonates and cyanides, and simple oxides, such as CO and CO2. Although a single, precise definition has yet to be
identified by the chemistry community, most agree that a defining trait of organic molecules is the presence of carbon as the principal
element, bonded to hydrogen and other carbon atoms.

Figure 1.0.1: All organic compounds contain carbon and most are formed by living things, although they are also formed by
geological and artificial processes. (credit left: modification of work by Jon Sullivan; credit left middle: modification of work by Deb
Tremper; credit right middle: modification of work by “annszyp”/Wikimedia Commons; credit right: modification of work by George
Shuklin)
Today, organic compounds are key components of plastics, soaps, perfumes, sweeteners, fabrics, pharmaceuticals, and many other
substances that we use every day. The value to us of organic compounds ensures that organic chemistry is an important discipline
within the general field of chemistry. In this chapter, we discuss why the element carbon gives rise to a vast number and variety of
compounds, how those compounds are classified, and the role of organic compounds in representative biological and industrial
settings.

CONTRIBUTORS
Paul Flowers (University of North Carolina - Pembroke), Klaus Theopold (University of Delaware) and Richard Langley (Stephen
F. Austin State University) with contributing authors. Textbook content produced by OpenStax College is licensed under a Creative
Commons Attribution License 4.0 license. Download for free at http://cnx.org/contents/[email protected]).
Dr. Dietmar Kennepohl FCIC (Professor of Chemistry, Athabasca University)

1.1.1 Updated 7/7/2019

1.2: ATOMIC STRUCTURE - THE NUCLEUS
OBJECTIVE
After completing this section, you should be able to describe the basic structure of the atom.

KEY TERMS
Make certain that you can define, and use in context, the key terms below.
atomic number
atomic weight
electron
mass number
neutron
proton

THE NUCLEAR ATOM

The precise physical nature of atoms finally emerged from a series of elegant experiments carried out between 1895 and 1915. The
most notable of these achievements was Ernest Rutherford's famous 1911 alpha-ray scattering experiment, which established that

Almost all of the mass of an atom is contained within a tiny (and therefore extremely dense) nucleus which carries a positive
electric charge whose value identifies each element and is known as the atomic number of the element.
Almost all of the volume of an atom consists of empty space in which electrons, the fundamental carriers of negative electric
charge, reside. The extremely small mass of the electron (1/1840th the mass of the hydrogen nucleus) causes it to behave as a
quantum particle, which means that its location at any moment cannot be specified; the best we can do is describe its behavior in
terms of the probability of its manifesting itself at any point in space. It is common (but somewhat misleading) to describe the
volume of space in which the electrons of an atom have a significant probability of being found as the electron cloud. The latter has
no definite outer boundary, so neither does the atom. The radius of an atom must be defined arbitrarily, such as the boundary in
which the electron can be found with 95% probability. Atomic radii are typically 30-300 pm.

PROTONS AND NEUTRONS

The nucleus is itself composed of two kinds of particles. Protons are the carriers of positive electric charge in the nucleus; the proton
charge is exactly the same as the electron charge, but of opposite sign. This means that in any [electrically neutral] atom, the number of
protons in the nucleus (often referred to as the nuclear charge) is balanced by the same number of electrons outside the nucleus.

Because the electrons of an atom are in contact with the outside world, it is possible for
one or more electrons to be lost, or some new ones to be added. The resulting electrically-
charged atom is called an ion.

The other nuclear particle is the neutron. As its name implies, this particle carries no electrical charge. Its mass is almost the same as
that of the proton. Most nuclei contain roughly equal numbers of neutrons and protons, so we can say that these two particles together
account for almost all the mass of the atom.

ATOMIC NUMBER (Z)

What single parameter uniquely characterizes the atom of a given element? It is not the atom's relative mass, as we will see in the
section on isotopes below. It is, rather, the number of protons in the nucleus, which we call the atomic number and denote by the

1.2.1 Updated 7/7/2019

symbol Z. Each proton carries an electric charge of +1, so the atomic number also specifies the electric charge of the nucleus. In the
neutral atom, the Z protons within the nucleus are balanced by Z electrons outside it.

Atomic numbers were first worked out in 1913 by Henry Moseley, a young member of Rutherford's research group in Manchester.
Moseley searched for a measurable property of each element that increases linearly with atomic number. He found this in a class of X-
rays emitted by an element when it is bombarded with electrons. The frequencies of these X-rays are unique to each element, and they
increase uniformly in successive elements. Moseley found that the square roots of these frequencies give a straight line when plotted
against Z; this enabled him to sort the elements in order of increasing atomic number.
You can think of the atomic number as a kind of serial number of an element, commencing at 1 for hydrogen and increasing by one for
each successive element. The chemical name of the element and its symbol are uniquely tied to the atomic number; thus the symbol
"Sr" stands for strontium, whose atoms all have Z = 38.

MASS NUMBER (A)

The mass number equals the sum of the numbers of protons and the number of neutrons in the nucleus. It is sometimes represented by
the symbol A, so

A = Z +N (1.2.1)

in which Z is the atomic number and N is the neutron number.

NUCLIDES AND THEIR SYMBOLS
The term nuclide simply refers to any particular kind of nucleus. For example, a nucleus of atomic number 7 is a nuclide of nitrogen.
Any nuclide is characterized by the pair of numbers (Z ,A). The element symbol depends on Z alone, so the symbol 26Mg is used to
specify the mass-26 nuclide of magnesium, whose name implies Z=12. A more explicit way of denoting a particular kind of nucleus is
to add the atomic number as a subscript. Of course, this is somewhat redundant, since the symbol Mg always implies Z=12, but it is
sometimes a convenience when discussing several nuclides.

Two nuclides having the same atomic number but different mass numbers are known as isotopes. Most elements occur in nature as
mixtures of isotopes, but twenty-three of them (including beryllium and fluorine, shown in the table) are monoisotopic. For example,
there are three natural isotopes of magnesium: 24Mg (79% of all Mg atoms), 25Mg (10%), and 26Mg (11%); all three are present in all
compounds of magnesium in about these same proportions.

Approximately 290 isotopes occur in nature. The two heavy isotopes of hydrogen are especially important— so much so that they have
names and symbols of their own:

1.2.2 Updated 7/7/2019

Deuterium accounts for only about 15 out of every one million atoms of hydrogen. Tritium, which is radioactive, is even less abundant.
All the tritium on the earth is a by-product of the decay of other radioactive elements.

ATOMIC WEIGHTS
Atoms are of course far too small to be weighed directly; weight measurements can only be made on the massive (but unknown)
numbers of atoms that are observed in chemical reactions. The early combining-weight experiments of Dalton and others established
that hydrogen is the lightest of the atoms, but the crude nature of the measurements and uncertainties about the formulas of many
compounds made it difficult to develop a reliable scale of the relative weights of atoms. Even the most exacting weight measurements
we can make today are subject to experimental uncertainties that limit the precision to four significant figures at best.

THE PERIODIC TABLE

The elements are arranged in a periodic table, which is probably the single most important learning aid in chemistry. It summarizes
huge amounts of information about the elements in a way that facilitates the prediction of many of their properties and chemical
reactions. The elements are arranged in seven horizontal rows, in order of increasing atomic number from left to right and top to
bottom. The rows are called periods, and they are numbered from 1 to 7. The elements are stacked in such a way that elements with
similar chemical properties form vertical columns, called groups, numbered from 1 to 18 (older periodic tables use a system based on
roman numerals). Groups 1, 2, and 13–18 are the main group elements, listed as A in older tables. Groups 3–12 are in the middle of the
periodic table and are the transition elements, listed as B in older tables. The two rows of 14 elements at the bottom of the periodic
table are the lanthanides and the actinides, whose positions in the periodic table are indicated in group 3.

CONTRIBUTORS
Dr. Dietmar Kennepohl FCIC (Professor of Chemistry, Athabasca University)
Prof. Steven Farmer (Sonoma State University)
William Reusch, Professor Emeritus (Michigan State U.), Virtual Textbook of Organic Chemistry
Organic Chemistry With a Biological Emphasis by Tim Soderberg (University of Minnesota, Morris)

1.2.3 Updated 7/7/2019

1.3: ATOMIC STRUCTURE - ORBITALS
OBJECTIVES
After completing this section, you should be able to
1. describe the physical significance of an orbital.
2. list the atomic orbitals from 1s to 3d in order of increasing energy.
3. sketch the shapes of s and p orbitals.

KEY TERMS
Make certain that you can define, and use in context, the key terms below.
nodal plane
node
orbital
quantum mechanics
wave function

For a refresher on quantum numbers view this text

ATOMIC ORBITALS
An orbital is the quantum mechanical refinement of Bohr’s orbit. In contrast to his concept of a simple circular orbit with a fixed
radius, orbitals are mathematically derived regions of space with different probabilities of having an electron.
One way of representing electron probability distributions was illustrated in Figure 6.5.2 for the 1s orbital of hydrogen. Because Ψ2
gives the probability of finding an electron in a given volume of space (such as a cubic picometer), a plot of Ψ2 versus distance from
the nucleus (r) is a plot of the probability density. The 1s orbital is spherically symmetrical, so the probability of finding a 1s electron
at any given point depends only on its distance from the nucleus. The probability density is greatest at r = 0 (at the nucleus) and
decreases steadily with increasing distance. At very large values of r, the electron probability density is very small but not zero.
In contrast, we can calculate the radial probability (the probability of finding a 1s electron at a distance r from the nucleus) by adding
together the probabilities of an electron being at all points on a series of x spherical shells of radius r1, r2, r3,…, rx − 1, rx. In effect, we
are dividing the atom into very thin concentric shells, much like the layers of an onion (part (a) in Figure 1.2.1), and calculating the
probability of finding an electron on each spherical shell. Recall that the electron probability density is greatest at r = 0 (part (b) in
Figure 1.2.1), so the density of dots is greatest for the smallest spherical shells in part (a) in Figure 1.2.1. In contrast, the surface area of
each spherical shell is equal to 4πr2, which increases very rapidly with increasing r (part (c) in Figure 1.2.1). Because the surface area
of the spherical shells increases more rapidly with increasing r than the electron probability density decreases, the plot of radial
probability has a maximum at a particular distance (part (d) in Figure 1.2.1). Most important, when r is very small, the surface area of a
spherical shell is so small that the total probability of finding an electron close to the nucleus is very low; at the nucleus, the electron
probability vanishes (part (d) in Figure 1.2.1).

1.3.1 Updated 7/7/2019

 Figure 1.2.1 Most Probable Radius for the Electron in the Ground State of the Hydrogen Atom. (a) Imagine dividing the atom’s total
volume into very thin concentric shells as shown in the onion drawing. (b) A plot of electron probability density Ψ2 versus r shows that
the electron probability density is greatest at r = 0 and falls off smoothly with increasing r. The density of the dots is therefore greatest
in the innermost shells of the onion. (c) The surface area of each shell, given by 4πr2, increases rapidly with increasing r. (d) If we
count the number of dots in each spherical shell, we obtain the total probability of finding the electron at a given value of r. Because
the surface area of each shell increases more rapidly with increasing r than the electron probability density decreases, a plot of
electron probability versus r (the radial probability) shows a peak. This peak corresponds to the most probable radius for the electron,
52.9 pm, which is exactly the radius predicted by Bohr’s model of the hydrogen atom.
For the hydrogen atom, the peak in the radial probability plot occurs at r = 0.529 Å (52.9 pm), which is exactly the radius calculated by
Bohr for the n = 1 orbit. Thus the most probable radius obtained from quantum mechanics is identical to the radius calculated by
classical mechanics. In Bohr’s model, however, the electron was assumed to be at this distance 100% of the time, whereas in the
quantum mechanical Schrödinger model, it is at this distance only some of the time. The difference between the two models is
attributable to the wavelike behavior of the electron and the Heisenberg uncertainty principle.
Figure 1.2.2 compares the electron probability densities for the hydrogen 1s, 2s, and 3s orbitals. Note that all three are spherically
symmetrical. For the 2s and 3s orbitals, however (and for all other s orbitals as well), the electron probability density does not fall off
smoothly with increasing r. Instead, a series of minima and maxima are observed in the radial probability plots (part (c) in Figure
1.2.2). The minima correspond to spherical nodes (regions of zero electron probability), which alternate with spherical regions of
nonzero electron probability.

1.3.2 Updated 7/7/2019

 Figure 1.2.2: Probability Densities for the 1s, 2s, and 3s Orbitals of the Hydrogen Atom. (a) The electron probability density in any
plane that contains the nucleus is shown. Note the presence of circular regions, or nodes, where the probability density is zero. (b)
Contour surfaces enclose 90% of the electron probability, which illustrates the different sizes of the 1s, 2s, and 3s orbitals. The
cutaway drawings give partial views of the internal spherical nodes. The orange color corresponds to regions of space where the phase
of the wave function is positive, and the blue color corresponds to regions of space where the phase of the wave function is negative.
(c) In these plots of electron probability as a function of distance from the nucleus (r) in all directions (radial probability), the most
probable radius increases as n increases, but the 2s and 3s orbitals have regions of significant electron probability at small values of r.

S ORBITALS
Three things happen to s orbitals as n increases (Figure 1.2.2):
1. They become larger, extending farther from the nucleus.
2. They contain more nodes. This is similar to a standing wave that has regions of significant amplitude separated by nodes, points
with zero amplitude.
3. For a given atom, the s orbitals also become higher in energy as n increases because of their increased distance from the nucleus.
Orbitals are generally drawn as three-dimensional surfaces that enclose 90% of the electron density, as was shown for the hydrogen 1s,
2s, and 3s orbitals in part (b) in Figure 1.2.2. Although such drawings show the relative sizes of the orbitals, they do not normally show
the spherical nodes in the 2s and 3s orbitals because the spherical nodes lie inside the 90% surface. Fortunately, the positions of the
spherical nodes are not important for chemical bonding.

P ORBITALS
Only s orbitals are spherically symmetrical. As the value of l increases, the number of orbitals in a given subshell increases, and the
shapes of the orbitals become more complex. Because the 2p subshell has l = 1, with three values of ml (−1, 0, and +1), there are three
2p orbitals.

1.3.3 Updated 7/7/2019

Figure 1.2.3: Electron Probability Distribution for a Hydrogen 2p Orbital. The nodal plane of zero electron density separates the two
lobes of the 2p orbital. As in Figure 1.2.2, the colors correspond to regions of space where the phase of the wave function is positive
(orange) and negative (blue).
The electron probability distribution for one of the hydrogen 2p orbitals is shown in Figure 1.2.3. Because this orbital has two lobes of
electron density arranged along the z axis, with an electron density of zero in the xy plane (i.e., the xy plane is a nodal plane), it is a 2pz
orbital. As shown in Figure 1.2.4, the other two 2p orbitals have identical shapes, but they lie along the x axis (2px) and y axis (2py),
respectively. Note that each p orbital has just one nodal plane. In each case, the phase of the wave function for each of the 2p orbitals is
positive for the lobe that points along the positive axis and negative for the lobe that points along the negative axis. It is important to
emphasize that these signs correspond to the phase of the wave that describes the electron motion, not to positive or negative charges.

Figure 1.2.4 The Three Equivalent 2p Orbitals of the Hydrogen Atom

The surfaces shown enclose 90% of the total electron probability for the 2px, 2py, and 2pz orbitals. Each orbital is oriented along the
axis indicated by the subscript and a nodal plane that is perpendicular to that axis bisects each 2p orbital. The phase of the wave
function is positive (orange) in the region of space where x, y, or z is positive and negative (blue) where x, y, or z is negative.
Just as with the s orbitals, the size and complexity of the p orbitals for any atom increase as the principal quantum number n increases.
The shapes of the 90% probability surfaces of the 3p, 4p, and higher-energy p orbitals are, however, essentially the same as those
shown in Figure 1.2.4.
The electron configuration of an atom is the representation of the arrangement of electrons distributed among the orbital shells and
subshells. Commonly, the electron configuration is used to describe the orbitals of an atom in its ground state, but it can also be used to
represent an atom that has ionized into a cation or anion by compensating with the loss of or gain of electrons in their subsequent
orbitals. Many of the physical and chemical properties of elements can be correlated to their unique electron configurations. The
valence electrons, electrons in the outermost shell, are the determining factor for the unique chemistry of the element.

ELECTRON CONFIGURATIONS
Before assigning the electrons of an atom into orbitals, one must become familiar with the basic concepts of electron configurations.
Every element on the periodic table consists of atoms, which are composed of protons, neutrons, and electrons. Electrons exhibit a
negative charge and are found around the nucleus of the atom in electron orbitals, defined as the volume of space in which the electron
can be found within 95% probability. The four different types of orbitals (s,p,d, and f) have different shapes, and one orbital can hold a
maximum of two electrons. The p, d, and f orbitals have different sublevels, thus can hold more electrons.
As stated, the electron configuration of each element is unique to its position on the periodic table. The energy level is determined by
the period and the number of electrons is given by the atomic number of the element. Orbitals on different energy levels are similar to
each other, but they occupy different areas in space. The 1s orbital and 2s orbital both have the characteristics of an s orbital (radial
nodes, spherical volume probabilities, can only hold two electrons, etc.) but, as they are found in different energy levels, they occupy
different spaces around the nucleus. Each orbital can be represented by specific blocks on the periodic table. The s-block is the region

1.3.4 Updated 7/7/2019

of the alkali metals including helium (Groups 1 & 2), the d-block are the transition metals (Groups 3 to 12), the p-block are the main
group elements from Groups 13 to 18, and the f-block are the lanthanides and actinides series.

Using the periodic table to determine the electron configurations of atoms is key, but also keep in mind that there are certain rules to
follow when assigning electrons to different orbitals. The periodic table is an incredibly helpful tool in writing electron configurations.
For more information on how electron configurations and the periodic table are linked, visit the Connecting Electrons to the Periodic
Table module.

RULES FOR ASSIGNING ELECTRON ORBITALS

OCCUPATION OF ORBITALS
Electrons fill orbitals in a way to minimize the energy of the atom. Therefore, the electrons in an atom fill the principal energy levels in
order of increasing energy (the electrons are getting farther from the nucleus). The relative energy of the orbitals is shown in Figure
1.2.5.

Figure 1.2.5 The relative potential energy of atomic orbitals

The order of levels filled is then:
1s, 2s, 2p, 3s, 3p, 4s, 3d, 4p, 5s, 4d, 5p, 6s, 4f, 5d, 6p, 7s, 5f, 6d, and 7p
One way to remember this pattern, and probably the easiest way, is to refer to the periodic table and remember where each orbital
block falls to logically deduce this pattern. Another way is to make a table like the one below and use vertical lines to determine which
subshells correspond with each other.

1.3.5 Updated 7/7/2019

THE NUMBER OF VALENCE ELECTRONS
The number of valence electrons of an element can be determined by the periodic table group (vertical column) in which the element is
categorized. With the exception of groups 3–12 (the transition metals), the units digit of the group number identifies how many valence
electrons are associated with a neutral atom of an element listed under that particular column. For example in group 16, the units digit
is 6 and elements in this group have 6 valence electrons.

The periodic table of the chemical elements

Periodic table group Valence electrons
Group 1: alkali metals 1

Group 2: alkaline earth metals 2

Groups 3-12: transition metals 2* (The 4s shell is complete and cannot hold any more electrons)

Group 13: boron group 3

Group 14: carbon group 4

Group 15: pnictogens 5

Group 16: chalcogens 6

Group 17: halogens 7

Group 18: noble gases 8**

* The general method for counting valence electrons is generally not useful for transition metals. Instead the modified d electron count
method is used.
** Except for helium, which has only two valence electrons.

1.3.6 Updated 7/7/2019

EXERCISES
Q1.2.1
Label the following orbitals:

Answer:

S1.2.1

1= 3px; 2= 3s ; 3= 2pz

CONTRIBUTORS
Dr. Dietmar Kennepohl FCIC (Professor of Chemistry, Athabasca University)
Prof. Steven Farmer (Sonoma State University)
William Reusch, Professor Emeritus (Michigan State U.), Virtual Textbook of Organic Chemistry
Organic Chemistry With a Biological Emphasis by Tim Soderberg (University of Minnesota, Morris)

1.3.7 Updated 7/7/2019

1.4: ATOMIC STRUCTURE - ELECTRON CONFIGURATIONS
OBJECTIVE
After completing this section, you should be able to write the ground-state electron configuration for each of the elements up to and
including atomic number 36.

KEY TERMS
Make certain that you can define, and use in context, the key terms below.
ground-state electronic configuration
Hund's rule
Pauli exclusion principle
aufbau principle

The electron configuration of an element is the arrangement of its electrons in its atomic orbitals. By knowing the electron
configuration of an element, we can predict and explain a great deal of its chemistry.

THE AUFBAU PRINCIPLE

We construct the periodic table by following the aufbau principle (from German, meaning “building up”). First we determine the
number of electrons in the atom; then we add electrons one at a time to the lowest-energy orbital available without violating the Pauli
principle. We use the orbital energy diagram of Figure 1.2.5, recognizing that each orbital can hold two electrons, one with spin up ↑,
corresponding to ms = +½, which is arbitrarily written first, and one with spin down ↓, corresponding to ms = −½. A filled orbital is
indicated by ↑↓, in which the electron spins are said to be paired. Here is a schematic orbital diagram for a hydrogen atom in its ground
state:

From the orbital diagram, we can write the electron configuration in an abbreviated form in which the occupied orbitals are identified
by their principal quantum number n and their value of l (s, p, d, or f), with the number of electrons in the subshell indicated by a
superscript. For hydrogen, the single electron is placed in the 1s orbital, which is the orbital lowest in energy (Figure 1.2.5), and the
electron configuration is written as 1s1 and read as “one-s-one.”
A neutral helium atom, with an atomic number of 2 (Z = 2), has two electrons. We place one electron in the orbital that is lowest in
energy, the 1s orbital. From the Pauli exclusion principle, we know that an orbital can contain two electrons with opposite spin, so we
place the second electron in the same orbital as the first but pointing down, so that the electrons are paired. The orbital diagram for the
helium atom is therefore

written as 1s2, where the superscript 2 implies the pairing of spins. Otherwise, our configuration would violate the Pauli principle.
The next element is lithium, with Z = 3 and three electrons in the neutral atom. We know that the 1s orbital can hold two of the
electrons with their spins paired. Figure 1.2.5 tells us that the next lowest energy orbital is 2s, so the orbital diagram for lithium is

This electron configuration is written as 1s22s1.

The next element is beryllium, with Z = 4 and four electrons. We fill both the 1s and 2s orbitals to achieve a 1s22s2 electron
configuration:

1.4.1 Updated 7/7/2019

When we reach boron, with Z = 5 and five electrons, we must place the fifth electron in one of the 2p orbitals. Because all three 2p
orbitals are degenerate, it doesn’t matter which one we select. The electron configuration of boron is 1s22s22p1:

At carbon, with Z = 6 and six electrons, we are faced with a choice. Should the sixth electron be placed in the same 2p orbital that
already has an electron, or should it go in one of the empty 2p orbitals? If it goes in an empty 2p orbital, will the sixth electron have its
spin aligned with or be opposite to the spin of the fifth? In short, which of the following three orbital diagrams is correct for carbon,
remembering that the 2p orbitals are degenerate?

Because of electron-electron repulsions, it is more favorable energetically for an electron to be in an unoccupied orbital than in one that
is already occupied; hence we can eliminate choice a. Similarly, experiments have shown that choice b is slightly higher in energy (less
stable) than choice c because electrons in degenerate orbitals prefer to line up with their spins parallel; thus, we can eliminate choice b.
Choice c illustrates Hund’s rule (named after the German physicist Friedrich H. Hund, 1896–1997), which says that the lowest-energy
electron configuration for an atom is the one that has the maximum number of electrons with parallel spins in degenerate orbitals. By
Hund’s rule, the electron configuration of carbon, which is 1s22s22p2, is understood to correspond to the orbital diagram shown in c.
Experimentally, it is found that the ground state of a neutral carbon atom does indeed contain two unpaired electrons.
When we get to nitrogen (Z = 7, with seven electrons), Hund’s rule tells us that the lowest-energy arrangement is

with three unpaired electrons. The electron configuration of nitrogen is thus 1s22s22p3.
At oxygen, with Z = 8 and eight electrons, we have no choice. One electron must be paired with another in one of the 2p orbitals,
which gives us two unpaired electrons and a 1s22s22p4 electron configuration. Because all the 2p orbitals are degenerate, it doesn’t
matter which one has the pair of electrons.

Similarly, fluorine has the electron configuration 1s22s22p5:

1.4.2 Updated 7/7/2019

When we reach neon, with Z = 10, we have filled the 2p subshell, giving a 1s22s22p6 electron configuration:

Notice that for neon, as for helium, all the orbitals through the 2p level are completely filled. This fact is very important in dictating
both the chemical reactivity and the bonding of helium and neon, as you will see.

VALENCE ELECTRONS
As we continue through the periodic table in this way, writing the electron configurations of larger and larger atoms, it becomes tedious
to keep copying the configurations of the filled inner subshells. In practice, chemists simplify the notation by using a bracketed noble
gas symbol to represent the configuration of the noble gas from the preceding row because all the orbitals in a noble gas are filled. For
example, [Ne] represents the 1s22s22p6 electron configuration of neon (Z = 10), so the electron configuration of sodium, with Z = 11,
which is 1s22s22p63s1, is written as [Ne]3s1:
Neon Z = 10 1s22s22p6
Sodium Z = 11 1s22s22p63s1 = [Ne]3s1

Because electrons in filled inner orbitals are closer to the nucleus and more tightly bound to it, they are rarely involved in chemical
reactions. This means that the chemistry of an atom depends mostly on the electrons in its outermost shell, which are called the valence
electrons. The simplified notation allows us to see the valence electron configuration more easily. Using this notation to compare the
electron configurations of sodium and lithium, we have:
Sodium 1s22s22p63s1 = [Ne]3s1
Lithium 1s22s1 = [He]2s1

It is readily apparent that both sodium and lithium have one s electron in their valence shell. We would therefore predict that sodium
and lithium have very similar chemistry, which is indeed the case.
As we continue to build the eight elements of period 3, the 3s and 3p orbitals are filled, one electron at a time. This row concludes with
the noble gas argon, which has the electron configuration [Ne]3s23p6, corresponding to a filled valence shell.

EXAMPLE 1.3.1
Draw an orbital diagram and use it to derive the electron configuration of phosphorus, Z = 15. What is its valence electron
configuration?
Given: atomic number
Asked for: orbital diagram and valence electron configuration for phosphorus
Strategy:
A. Locate the nearest noble gas preceding phosphorus in the periodic table. Then subtract its number of electrons from those in
phosphorus to obtain the number of valence electrons in phosphorus.
B. Referring to Figure 1.3.1, draw an orbital diagram to represent those valence orbitals. Following Hund’s rule, place the valence
electrons in the available orbitals, beginning with the orbital that is lowest in energy. Write the electron configuration from your
orbital diagram.
C. Ignore the inner orbitals (those that correspond to the electron configuration of the nearest noble gas) and write the valence
electron configuration for phosphorus.
Solution:
A Because phosphorus is in the third row of the periodic table, we know that it has a [Ne] closed shell with 10 electrons. We begin
by subtracting 10 electrons from the 15 in phosphorus.
B The additional five electrons are placed in the next available orbitals, which Figure 1.2.5 tells us are the 3s and 3p orbitals:

1.4.3 Updated 7/7/2019

 Because the 3s orbital is lower in energy than the 3p orbitals, we fill it first:

Hund’s rule tells us that the remaining three electrons will occupy the degenerate 3p orbitals separately but with their spins aligned:

The electron configuration is [Ne]3s23p3.

C We obtain the valence electron configuration by ignoring the inner orbitals, which for phosphorus means that we ignore the [Ne]
closed shell. This gives a valence-electron configuration of 3s23p3.

EXERCISE 1.3.1
Draw an orbital diagram and use it to derive the electron configuration of chlorine, Z = 17. What is its valence electron
configuration?

Answer:
[Ne]3s23p5; 3s23p5

The general order in which orbitals are filled is depicted in Figure 1.3.1. Subshells corresponding to each value of n are written from
left to right on successive horizontal lines, where each row represents a row in the periodic table. The order in which the orbitals are
filled is indicated by the diagonal lines running from the upper right to the lower left. Accordingly, the 4s orbital is filled prior to the 3d
orbital because of shielding and penetration effects. Consequently, the electron configuration of potassium, which begins the fourth
period, is [Ar]4s1, and the configuration of calcium is [Ar]4s2. Five 3d orbitals are filled by the next 10 elements, the transition metals,
followed by three 4p orbitals. Notice that the last member of this row is the noble gas krypton (Z = 36), [Ar]4s23d104p6 = [Kr], which
has filled 4s, 3d, and 4p orbitals. The fifth row of the periodic table is essentially the same as the fourth, except that the 5s, 4d, and 5p
orbitals are filled sequentially.

Figure 1.3.1: Predicting the Order in Which Orbitals Are Filled in Multielectron Atoms. If you write the subshells for each value of the
principal quantum number on successive lines, the observed order in which they are filled is indicated by a series of diagonal lines
running from the upper right to the lower left.
The sixth row of the periodic table will be different from the preceding two because the 4f orbitals, which can hold 14 electrons, are
filled between the 6s and the 5d orbitals. The elements that contain 4f orbitals in their valence shell are the lanthanides. When the 6p
orbitals are finally filled, we have reached the next (and last known) noble gas, radon (Z = 86), [Xe]6s24f145d106p6 = [Rn]. In the last
row, the 5f orbitals are filled between the 7s and the 6d orbitals, which gives the 14 actinide elements. Because the large number of
protons makes their nuclei unstable, all the actinides are radioactive.

EXAMPLE 1.3.2
Write the electron configuration of mercury (Z = 80), showing all the inner orbitals.

1.4.4 Updated 7/7/2019

 Given: atomic number
Asked for: complete electron configuration
Strategy:
Using the orbital diagram in Figure 1.3.1 and the periodic table as a guide, fill the orbitals until all 80 electrons have been placed.
Solution:
By placing the electrons in orbitals following the order shown in Figure 1.3.1 and using the periodic table as a guide, we obtain
1s2 row 1 2 electrons
2s22p6 row 2 8 electrons
3s23p6 row 3 8 electrons
4s23d104p6 row 4 18 electrons
5s24d105p6 row 5 18 electrons
row 1–5 54 electrons
After filling the first five rows, we still have 80 − 54 = 26 more electrons to accommodate. According to Figure 1.3.1, we need to
fill the 6s (2 electrons), 4f (14 electrons), and 5d (10 electrons) orbitals. The result is mercury’s electron configuration:
1s22s22p63s23p64s23d104p65s24d105p66s24f145d10 = Hg = [Xe]6s24f145d10
with a filled 5d subshell, a 6s24f145d10 valence shell configuration, and a total of 80 electrons. (You should always check to be sure
that the total number of electrons equals the atomic number.)

SUMMARY
Based on the Pauli principle and a knowledge of orbital energies obtained using hydrogen-like orbitals, it is possible to construct the
periodic table by filling up the available orbitals beginning with the lowest-energy orbitals (the aufbau principle), which gives rise to
a particular arrangement of electrons for each element (its electron configuration). Hund’s rule says that the lowest-energy
arrangement of electrons is the one that places them in degenerate orbitals with their spins parallel. For chemical purposes, the most
important electrons are those in the outermost principal shell, the valence electrons.

EXERCISES
QUESTIONS
Q1.3.1
Give the electron configurations for Al, Br, Fe.
SOLUTIONS
S1.3.1
Al = 1s22s22p63s23p1
Br = 1s22s22p63s23p64s23d104p5
Fe = 1s22s22p63s23p64s23d6

CONTRIBUTORS
Dr. Dietmar Kennepohl FCIC (Professor of Chemistry, Athabasca University)
Prof. Steven Farmer (Sonoma State University)
William Reusch, Professor Emeritus (Michigan State U.), Virtual Textbook of Organic Chemistry
Organic Chemistry With a Biological Emphasis by Tim Soderberg (University of Minnesota, Morris)

1.4.5 Updated 7/7/2019

1.5: DEVELOPMENT OF CHEMICAL BONDING THEORY
OBJECTIVES
After completing this section, you should be able to
1. draw Lewis Dot Symbols for main group elements and ions.
2. describe the three-dimensional nature of molecules.
3. sketch a tetrahedral molecule, CX4, using the “wedge-and-broken-line” method of representation.
4. make a ball-and-stick model of a simple tetrahedral molecule such as methane, CH4.
5. draw Lewis Dot Structures for 2 electron group molecules.
6. draw Lewis Dot Structures for 3 electron group molecules.
7. draw Lewis Dot Structures for 4 electron group molecules.

STUDY NOTES
When drawing any organic structure, you must remember that a neutral carbon atom will almost always have four bonds. Similarly,
hydrogen always has one bond; neutral oxygen atoms have two bonds; and neutral nitrogen atoms have three bonds. By committing
these simple rules to memory, you can avoid making unnecessary mistakes later in the course.
The “wedge-and-broken-line” type of representation, which helps to convey the three-dimensional nature of organic compounds,
will be used throughout the course.

BONDING OVERVIEW
Why are some substances chemically bonded molecules and others are an association of ions? The answer to this question depends
upon the electronic structures of the atoms and nature of the chemical forces within the compounds. Although there are no sharply
defined boundaries, chemical bonds are typically classified into three main types: ionic bonds, covalent bonds, and metallic bonds. In
this chapter, each type of bond and the general properties found in typical substances in which the bond type occurs will be discussed.
1. Ionic bonds results from electrostatic forces that exist between ions of opposite charge. These bonds typically involve a metal with
a nonmetal
2. Covalent bonds result from the sharing of electrons between two atoms. The bonds typically involve one nonmetallic element with
another
3. Metallic bonds are found in solid metals (copper, iron, aluminum) with each metal atom bonded to several neighboring metal atoms
and the bonding electrons are free to move throughout the 3-dimensional structure.
Each bond classification is discussed in detail in subsequent sections of the chapter. Let's look at the preferred arrangements of
electrons in atoms when they form chemical compounds.

Figure 1.4.1: G. N. Lewis and the Octet Rule. (a) Lewis is working in the laboratory. (b) In Lewis’s original sketch for the octet rule,
he initially placed the electrons at the corners of a cube rather than placing them as we do now.

LEWIS SYMBOLS
At the beginning of the 20th century, the American chemist G. N. Lewis (1875–1946) devised a system of symbols—now called Lewis
electron dot symbols, often shortened to Lewis dot symbols—that can be used for predicting the number of bonds formed by most
elements in their compounds. Each Lewis dot symbol consists of the chemical symbol for an element surrounded by dots that represent
its valence electrons.

LEWIS DOT SYMBOLS:

1.5.1 Updated 7/7/2019

 provide a convenient representation of valence electrons
allows you to keep track of valence electrons during bond formation
consists of the chemical symbol for the element plus a dot for each valence electron

To write an element’s Lewis dot symbol, we place dots representing its valence electrons, one at a time, around the element’s chemical
symbol. Up to four dots are placed above, below, to the left, and to the right of the symbol (in any order, as long as elements with four
or fewer valence electrons have no more than one dot in each position). The next dots, for elements with more than four valence
electrons, are again distributed one at a time, each paired with one of the first four. For example, the electron configuration for atomic
sulfur is [Ne]3s23p4, thus there are six valence electrons. Its Lewis symbol would therefore be:

Fluorine, for example, with the electron configuration [He]2s22p5, has seven valence electrons, so its Lewis dot symbol is constructed
as follows:

The number of dots in the Lewis dot symbol is the same as the number of valence electrons, which is the same as the last digit of the
element’s group number in the periodic table. Lewis dot symbols for the elements in period 2 are given in Figure 1.4.2.
Lewis used the unpaired dots to predict the number of bonds that an element will form in a compound. Consider the symbol for
nitrogen in Figure 1.4.2. The Lewis dot symbol explains why nitrogen, with three unpaired valence electrons, tends to form compounds
in which it shares the unpaired electrons to form three bonds. Boron, which also has three unpaired valence electrons in its Lewis dot
symbol, also tends to form compounds with three bonds, whereas carbon, with four unpaired valence electrons in its Lewis dot symbol,
tends to share all of its unpaired valence electrons by forming compounds in which it has four bonds.

Figure 1.4.2: Lewis Dot Symbols for the Elements in Period 2

THE OCTET RULE

Lewis’s major contribution to bonding theory was to recognize that atoms tend to lose, gain, or share electrons to reach a total of eight
valence electrons, called an octet. This so-called octet rule explains the stoichiometry of most compounds in the s and p blocks of the
periodic table. We now know from quantum mechanics that the number eight corresponds to one ns and three np valence orbitals,
which together can accommodate a total of eight electrons. Remarkably, though, Lewis’s insight was made nearly a decade before
Rutherford proposed the nuclear model of the atom. Common exceptions to the octet rule are helium, whose 1s2 electron configuration
gives it a full n = 1 shell, and hydrogen, which tends to gain or share its one electron to achieve the electron configuration of helium.
Lewis dot symbols can also be used to represent the ions in ionic compounds. The reaction of cesium with fluorine, for example, to
produce the ionic compound CsF can be written as follows:

1.5.2 Updated 7/7/2019

No dots are shown on Cs+ in the product because cesium has lost its single valence electron to fluorine. The transfer of this electron
produces the Cs+ ion, which has the valence electron configuration of Xe, and the F− ion, which has a total of eight valence electrons
(an octet) and the Ne electron configuration. This description is consistent with the statement that among the main group elements, ions
in simple binary ionic compounds generally have the electron configurations of the nearest noble gas. The charge of each ion is written
in the product, and the anion and its electrons are enclosed in brackets. This notation emphasizes that the ions are associated
electrostatically; no electrons are shared between the two elements.

Atoms often gain, lose, or share electrons to achieve the same number of electrons as the
noble gas closest to them in the periodic table.

MOLECULAR SHAPE
A stick and wedge drawing of methane shows the tetrahedral angles...(The wedge is coming out of the paper and the dashed line is
going behind the paper. The solid lines are in the plane of the paper.)

The following examples make use of this notation, and also illustrate the importance of including non-bonding valence shell electron
pairs when viewing such configurations.

Methane Ammonia Water

Bonding configurations are readily predicted by valence-shell electron-pair repulsion theory, commonly referred to as VSEPR in most
introductory chemistry texts. This simple model is based on the fact that electrons repel each other, and that it is reasonable to expect
that the bonds and non-bonding valence electron pairs associated with a given atom will prefer to be as far apart as possible. The
bonding configurations of carbon are easy to remember, since there are only three categories.
Configuration Bonding Partners Bond Angles Example

Tetrahedral 4 109.5º

Trigonal Planar 3 120º

Linear 2 180º

Figure 1.4.3 In the three examples shown above, the central atom (carbon) does not have any non-bonding valence electrons;
consequently the configuration may be estimated from the number of bonding partners alone. However, for molecules of water and

1.5.3 Updated 7/7/2019

ammonia, the non-bonding electrons must be included in the calculation. In each case there are four regions of electron density
associated with the valence shell so that a tetrahedral bond angle is expected. The measured bond angles of these compounds (H2O
104.5º & NH3 107.3º) show that they are closer to being tetrahedral than trigonal planar or linear. Of course, it is the configuration of
atoms (not electrons) that defines the the shape of a molecule, and in this sense ammonia is said to be pyramidal (not tetrahedral). The
compound boron trifluoride, BF3, does not have non-bonding valence electrons and the configuration of its atoms is trigonal. Nice
treatments of VSEPR theory have been provided by Oxford and Purdue. The best way to study the three-dimensional shapes of
molecules is by using molecular models. Many kinds of model kits are available to students and professional chemists.

TWO ELECTRON GROUPS

Our first example is a molecule with two bonded atoms and no lone pairs of electrons, .

AX2: BEH2
1. The central atom, beryllium, contributes two valence electrons, and each hydrogen atom contributes one. The Lewis electron
structure is

Figure 1.4.4: Lewis Structure for BeH2

2. There are two electron groups around the central atom. We see from Figure 1.4.3 that the arrangement that minimizes repulsions
places the groups 180° apart.
3. Both groups around the central atom are bonding pairs (BP). Thus BeH2 is designated as AX2.
4. From Figure 1.4.3 we see that with two bonding pairs, the molecular geometry that minimizes repulsions in BeH2 is linear.

AX2: CO2
1. The central atom, carbon, contributes four valence electrons, and each oxygen atom contributes six. The Lewis electron structure is

2. The carbon atom forms two double bonds. Each double bond is a group, so there are two electron groups around the central atom.
Like BeH2, the arrangement that minimizes repulsions places the groups 180° apart.
3. Once again, both groups around the central atom are bonding pairs (BP), so CO2 is designated as AX2.
4. VSEPR only recognizes groups around the central atom. Thus the lone pairs on the oxygen atoms do not influence the molecular
geometry. With two bonding pairs on the central atom and no lone pairs, the molecular geometry of CO2 is linear (Figure 1.4.3).

THREE ELECTRON GROUPS

AX3: BCL3
1. The central atom, boron, contributes three valence electrons, and each chlorine atom contributes seven valence electrons. The Lewis
electron structure is

2. There are three electron groups around the central atom. To minimize repulsions, the groups are placed 120° apart (Figure 1.4.3).
3. All electron groups are bonding pairs (BP), so the structure is designated as AX3.
4. From Figure 1.4.3 we see that with three bonding pairs around the central atom, the molecular geometry of BCl3 is trigonal planar.

AX3: CO32−
1. The central atom, carbon, has four valence electrons, and each oxygen atom has six valence electrons. As you learned previously, the
Lewis electron structure of one of three resonance forms is represented as

1.5.4 Updated 7/7/2019

2. The structure of CO32− is a resonance hybrid. It has three identical bonds, each with a bond order of 4/3. We minimize repulsions
by placing the three groups 120° apart (Figure 1.4.3).
3. All electron groups are bonding pairs (BP). With three bonding groups around the central atom, the structure is designated as AX3.
4. We see from Figure 1.4.3 that the molecular geometry of CO32− is trigonal planar.

In our next example we encounter the effects of lone pairs and multiple bonds on molecular geometry for the first time.
AX2E: SO2
1. The central atom, sulfur, has 6 valence electrons, as does each oxygen atom. With 18 valence electrons, the Lewis electron structure
is shown below.

2. There are three electron groups around the central atom, two double bonds and one lone pair. We initially place the groups in a
trigonal planar arrangement to minimize repulsions (Figure 1.4.3).
3. There are two bonding pairs and one lone pair, so the structure is designated as AX2E. This designation has a total of three electron
pairs, two X and one E. Because a lone pair is not shared by two nuclei, it occupies more space near the central atom than a bonding
pair (Figure 1.4.4). Thus bonding pairs and lone pairs repel each other electrostatically in the order BP–BP < LP–BP < LP–LP. In SO2,
we have one BP–BP interaction and two LP–BP interactions.
4. The molecular geometry is described only by the positions of the nuclei, not by the positions of the lone pairs. Thus with two nuclei
and one lone pair the shape is bent, or V shaped, which can be viewed as a trigonal planar arrangement with a missing vertex (Figures
1.4.2.1 and 1.4.3).

Figure 1.4.4: The Difference in the Space Occupied by a Lone Pair of Electrons and by a Bonding Pair
As with SO2, this composite model of electron distribution and negative electrostatic potential in ammonia shows that a lone pair of
electrons occupies a larger region of space around the nitrogen atom than does a bonding pair of electrons that is shared with a

1.5.5 Updated 7/7/2019

hydrogen atom.
Like lone pairs of electrons, multiple bonds occupy more space around the central atom than a single bond, which can cause other bond
angles to be somewhat smaller than expected. This is because a multiple bond has a higher electron density than a single bond, so its
electrons occupy more space than those of a single bond. For example, in a molecule such as CH2O (AX3), whose structure is shown
below, the double bond repels the single bonds more strongly than the single bonds repel each other. This causes a deviation from ideal
geometry (an H–C–H bond angle of 116.5° rather than 120°).

FOUR ELECTRON GROUPS

One of the limitations of Lewis structures is that they depict molecules and ions in only two dimensions. With four electron groups, we
must learn to show molecules and ions in three dimensions.

AX4: CH4
1. The central atom, carbon, contributes four valence electrons, and each hydrogen atom has one valence electron, so the full Lewis
electron structure is

2. There are four electron groups around the central atom. As shown in Figure 1.4.2, repulsions are minimized by placing the groups in
the corners of a tetrahedron with bond angles of 109.5°.
3. All electron groups are bonding pairs, so the structure is designated as AX4.
4. With four bonding pairs, the molecular geometry of methane is tetrahedral (Figure 1.4.3).

AX3E: NH3
1. In ammonia, the central atom, nitrogen, has five valence electrons and each hydrogen donates one valence electron, producing the
Lewis electron structure

2. There are four electron groups around nitrogen, three bonding pairs and one lone pair. Repulsions are minimized by directing each
hydrogen atom and the lone pair to the corners of a tetrahedron.
3. With three bonding pairs and one lone pair, the structure is designated as AX3E. This designation has a total of four electron pairs,
three X and one E. We expect the LP–BP interactions to cause the bonding pair angles to deviate significantly from the angles of a
perfect tetrahedron.

1.5.6 Updated 7/7/2019

4. There are three nuclei and one lone pair, so the molecular geometry is trigonal pyramidal. In essence, this is a tetrahedron with a
vertex missing (Figure 1.4.3). However, the H–N–H bond angles are less than the ideal angle of 109.5° because of LP–BP repulsions.

AX2E2: H2O
1. Oxygen has six valence electrons and each hydrogen has one valence electron, producing the Lewis electron structure

2. There are four groups around the central oxygen atom, two bonding pairs and two lone pairs. Repulsions are minimized by directing
the bonding pairs and the lone pairs to the corners of a tetrahedron Figure 1.4.3.
3. With two bonding pairs and two lone pairs, the structure is designated as AX2E2 with a total of four electron pairs. Due to LP–LP,
LP–BP, and BP–BP interactions, we expect a significant deviation from idealized tetrahedral angles.
4. With two hydrogen atoms and two lone pairs of electrons, the structure has significant lone pair interactions. There are two nuclei
about the central atom, so the molecular shape is bent, or V shaped, with an H–O–H angle that is even less than the H–N–H angles in
NH3, as we would expect because of the presence of two lone pairs of electrons on the central atom rather than one.. This molecular
shape is essentially a tetrahedron with two missing vertices.

EXERCISES
QUESTIONS
Q1.4.1
List the bond angles for each of the following compounds: BH3, CF4, H2O.
Q1.4.2
Why is sulfur dioxide a bent molecule (bond angle less than 180°)?
SOLUTIONS
S1.4.1
HBH = 120°
FCF = 109.5°
OHO = 104°
S1.4.2
This deviation is due to the lone pairs on the sulfur. These force the molecule to exhibit a
“bent” geometry and therefore a deviation from the 180°.

1.5.7 Updated 7/7/2019

1.6: THE NATURE OF CHEMICAL BONDS - VALENCE BOND THEORY
OBJECTIVES
After completing this section, you should be able to
1. explain how covalent bonds are formed as a result of the ability of atoms to share electrons.
2. draw Lewis structures (also known as Lewis formulas or electron-dot formulas) of simple species, such as CH4, H2O, H3O+,
CH3OH, and NH3, without the aid of a periodic table.
3. draw structural formulas (i.e., Kekulé structures or line-bond structures) of simple species without the aid of a periodic table.
4. describe the formation of covalent bonds in terms of the overlapping of atomic orbitals.

KEY TERMS
Make certain that you can define, and use in context, the key terms below.
bond strength
covalent bond
ionic bond
Lewis structure
lone-pair electron
non-bonding electron
sigma (σ) bond

π
pi ( ) bond
valence bond theory

STUDY NOTES
To draw Lewis structures successfully, you need to know the number of valence electrons present in each of the atoms involved.
Memorize the number of valence electrons possessed by each of the elements commonly encountered in organic chemistry: C, H,
O, N, S, P and the halogens.

IONIC BONDING
Ions are atoms or molecules which are electrically charged. Cations are positively charged and anions carry a negative charge. Ions
form when atoms gain or lose electrons. Since electrons are negatively charged, an atom that loses one or more electrons will become
positively charged; an atom that gains one or more electrons becomes negatively charged.
Ionic bonding is the attraction between positively- and negatively-charged ions. These oppositely charged ions attract each other to
form ionic networks (or lattices). Electrostatics explains why this happens: opposite charges attract and like charges repel. When many
ions attract each other, they form large, ordered, crystal lattices in which each ion is surrounded by ions of the opposite charge.
Generally, when metals react with non-metals, electrons are transferred from the metals to the non-metals. The metals form positively-
charged ions and the non-metals form negatively-charged ions.
Ionic bonds form when metals and non-metals chemically react. By definition, a metal is relatively stable if it loses electrons to form a
complete valence shell and becomes positively charged. Likewise, a non-metal becomes more stable by gaining electrons to complete
its valence shell and become negatively charged. When metals and non-metals react, the metals lose electrons by transferring them to
the non-metals, which gain them. Consequently, ions are formed, which instantly attract each other—ionic bonding.

EXAMPLE 1.5.1: SODIUM CHLORIDE

For example, in the reaction of Na (sodium) and Cl (chlorine), each Cl atom takes one electron from a Na atom. Therefore each Na
becomes a Na+ cation and each Cl atom becomes a Cl- anion. Due to their opposite charges, the ions of sodium and chloride attract
each other to form an ionic lattice. The formula (ratio of positive to negative ions) in the lattice is NaCl.

For full video of making NaCl from sodium metal and chlorine gase, see https://www.youtube.com/watch?v=WVonuBjCrNo. These
ions are arranged in solid NaCl in a regular three-dimensional arrangement (or lattice):

1.6.1 Updated 7/7/2019

 Figure: NaCl lattice. (left) 3-D structure and (right) simple 2D slice through lattes. Images used with permission from Wikipedia
and Mike Blaber.
The chlorine has a high affinity for electrons, and the sodium has a low ionization potential. Thus the chlorine gains an electron
from the sodium atom. This can be represented using electron-dot symbols (here we will consider one chlorine atom, rather than
Cl2):

The arrow indicates the transfer of the electron from sodium to chlorine to form the Na+ metal ion and the Cl- chloride ion. Each ion
now has an octet of electrons in its valence shell:
Na+: 2s22p6
Cl-: 3s23p6

THE IMPORTANCE OF NOBLE GAS STRUCTURES

A lot of importance is attached to the electronic structures of noble gases like neon or argon which have eight electrons in their
outer energy levels (or two in the case of helium). These noble gas structures are thought of as being in some way a "desirable"
thing for an atom to have. You may well have been left with the strong impression that when other atoms react, they try to achieve
noble gas structures. As well as achieving noble gas structures by transferring electrons from one atom to another as in ionic
bonding, it is also possible for atoms to reach these stable structures by sharing electrons to give covalent bonds.

CHEMICAL BONDS
Chemical bonds are the attractive forces that hold atoms together in the form of compounds. They are formed when electrons are
shared between two atoms. There are 3 types of bonds: covalent bonds, polar covalent bonds and ionic bonds. The simplest example of
bonding can be demonstrated by the H2 molecule. We can see from the periodic table that each hydrogen atom has a single electron. If
2 hydrogen atoms come together to form a bond, then each hydrogen atom effectively has a share in both electrons and thus each
resembles a noble gas and is more stable. The 2 electrons that are shared can be represented either by 2 dots or a single dash between
the atoms.

Valence bond theory describes a chemical bond as the overlap of atomic orbitals. In the case of the hydrogen molecule, the 1s orbital of
one hydrogen atom overlaps with the 1s orbital of the second hydrogen atom to form a molecular orbital called a sigma bond.
Attraction increases as the distance between the atoms gets closer but nuclear-nuclear repulsion becomes important if the atoms
approach too close.

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There are 3 methods of showing the formulas of molecules. Molecular formulas show only the types and numbers of atoms in the
molecule. Structural formulas show the atoms in their correct placement in the molecule and allow for distinguishing isomers.
Electron-dot formulas are similar to structural formulas but also include all of the non-bonding outer electrons. Knowledge of electron
placement allows us to understand not only the shape of molecules but their chemical character. If we understand the chemical
character of a molecule, we can predict how it will react with other molecules without having to blindly memorize reactions.

COVALENT BONDS AND LEWIS STRUCTURES

Lewis structures, also known as Lewis-dot diagrams, show the bonding relationship between atoms of a molecule and the lone pairs of
electrons in the molecule. Lewis structures can also be useful in predicting molecular geometry in conjunction with hybrid orbitals. A
compound may have multiple resonance forms that are also all correct Lewis structures. This section will discuss the rules for correctly
writing Lewis structures.
Before we begin, there are a few things to know. An electron is represented as a dot. A bond, which is made up of 2 shared electrons, is
represented by two dots between the bonded atoms or a line. Double bonds and triple bonds are represented as two and three lines
(pairs of electrons), respectively. Lone pairs on the outer rims of an atom are represented as two dots. The electrons represented in a
Lewis structure are the outer-shell electrons, which are called valence electrons. This is because they are the ones involved in chemical
reactions.
While alkali metals (such as sodium and potassium), alkaline earth metals (such as magnesium and calcium), and halogens (such as
fluorine and chlorine) often form ions in order to achieve a full octet, the principle elements of organic chemistry - carbon, hydrogen,
nitrogen, and oxygen - instead tend to fill their second shell orbitals by sharing electrons with other atoms, forming what we call
covalent bonds. Consider the simplest case of hydrogen gas. An isolated hydrogen atom has only one electron, located in the 1s orbital.
If two hydrogen atoms come close enough so that their respective 1s orbitals overlap, the two electrons can be shared between the two
nuclei, and a covalently bonded H2 molecule is formed. In the ‘Lewis method’, each pair of electrons that is shared between two atoms
is drawn as a single line, designating a single covalent bond.

Hydrogen represents is a special case, of course – a hydrogen atom cannot fulfill the octet rule; it needs only two electrons to have a
full shell (you could think of this as the ‘doublet rule’ for hydrogen).
One of the simplest organic molecules is methane with the molecular formula CH4. Methane is the ‘natural gas’ burned in home
furnaces and hot water heaters, as well as in electrical power generating plants. To illustrate the covalent bonding in methane using the
Lewis method, we first must recognize that, although a carbon atom has a total of six electrons, the two electrons in the inner 1s orbital
do not participate in bonding interactions. It is the other four- those in the 2s and 2p orbitals - that form covalent bonds with other
atoms. Only the partially occupied, highest energy shell of orbitals - in this case the 2s and 2p orbitals - can overlap with orbitals on
other atoms to form covalent bonds. Electrons in these orbitals are termed ‘valence electrons’.

A carbon atom, then, has four valence electrons with which to form covalent bonds. In order to fulfill the octet rule and increase the
occupancy of its second shell to eight electrons, it must participate in four electron-sharing interactions - in other words, it must form
four covalent bonds. In a methane molecule, the central carbon atom shares its four valence electrons with four hydrogen atoms, thus
forming four bonds and fulfilling the octet rule (for the carbon) and the ‘doublet rule’ (for each of the hydrogens).

The next relatively simple organic molecule to consider is ethane, which has the molecular formula C2H6. If we draw each atom with
its valence electron(s) separately, we can see that the octet/doublet rule can be fulfilled for all of them by forming one carbon-carbon
bond and six carbon-hydrogen bonds.

1.6.3 Updated 7/7/2019

The same approach can be used for molecules in which there is no carbon atom. In a water molecule, two of the six valence electrons
on the oxygen atom are used to form bonds to hydrogen atoms, while the remaining four are non-bonding ‘lone pairs’.

EXERCISE 1.5.1
Draw the Lewis structure for ammonia, NH3.

Answer:

What about multiple bonds? The molecular formula for ethene (also known as ethylene, a compound found in fruits,
such as apples, that signals them to ripen) is C2H4. Arranging the atoms and surrounding them with their valence
electrons, you can see that the octet/doublet rule can be fulfilled for all atoms only if the two carbons share two pairs
of electrons between them - in other words, only if a double bond is formed.

Because a hydrogen atom has only a 1s orbital to work with, it cannot form more than one single bond, otherwise it would exceed its
doublet rule.
Following this pattern, the triple bond in ethyne molecular formula C2H2, (also known as acetylene, the fuel used in welding torches),
is formed when the two carbon atoms share three pairs of electrons between them.

What about ions? The hydroxide ion, OH-, is drawn simply by showing the oxygen atom with its six valence electrons, then adding one
more electron to account for the negative charge. Now the oxygen has three non-bonding lone pairs, and can only form one bond to a
hydrogen. (Bear in mind that this is merely a description of the thought process going into drawing a Lewis structure, and is not meant
to describe any actual chemical process).

To draw a Lewis structure of the hydronium ion, H3O+, you again start with the oxygen atom with its six valence electrons, then take
one away to account for the positive charge (there is now one more proton than there are electrons). The oxygen now can form bonds
to three hydrogen atoms.

EXERCISE 1.5.2
Draw a Lewis structure for the ammonium ion, NH4+.

Answer:

1.6.4 Updated 7/7/2019

 EXERCISE 1.5.3
Draw Lewis structures for neutral molecules with the connectivity shown below. Show all lone pairs. The octet rule should be
fulfilled for all atoms.

Answer:

FORMAL CHARGES
Consider the Lewis structure of methanol, CH3OH (methanol is the so-called ‘wood alcohol’ that unscrupulous bootleggers sometimes
sold during the Prohibition days, often causing the people who drank it to go blind). Just like in a water molecule, the oxygen atom in a
methanol molecule has two non-bonding lone pairs of electrons. And just like a water molecule can be protonated to form the H3O+
cation, a methanol molecule can be protonated to form the CH3OH2+ cation.

This polyatomic cation, as you can see, has an overall charge of +1. But we can be more specific than that - we can also state that the
positive charge is located specifically on the oxygen atom, rather than on the carbon or any of the hydrogens. When a charge can be
located on a particular atom in a polyatomic ion, this atom is said to have a ‘formal charge’. Figuring out the formal charge on different
atoms of a polyatomic ion is a straightforward process - it’s simply a matter of adding up valence electrons. Remember that an oxygen
atom needs six valence electrons (in addition to the two electrons in the non-valence 1s orbital) to completely balance the charge of the
eight protons in its nucleus. Let’s figure out how many electrons the oxygen atom in our CH3OH2+ ion ‘owns’.

1.6.5 Updated 7/7/2019

First, we see that there is one lone pair of electrons that the oxygen is not sharing with any other atom - thus it 'owns' both of these
electrons. In addition, the oxygen atom is sharing one pair of electrons each with three other atoms - since these electrons are shared,
we decide that oxygen 'owns' one electron from each pair, meaning that it owns three bonding electrons. In total then, the oxygen owns
five valence electrons: two non-bonding and three bonding. This is one short of the six valence electrons needed to achieve neutrality -
thus the oxygen atom has a formal charge of +1.
What is the formal charge, if any, on the other atoms? The carbon needs to ‘own’ four valence electrons (once again, in addition to the
two electrons in its 1s orbital) in order to balance the six protons in its nucleus. Because the carbon atom has four single bonds in this
structure, and no lone pairs, it does indeed own four electrons (remember that it owns one of each pair of electrons that it shares in a
covalent bond). So the carbon has a formal charge of zero.
Each hydrogen needs to own only one electron to balance the charge of its single proton. Indeed, in the CH3OH2+ structure, each
hydrogen atom has one single bond, meaning that each one owns one electron. Thus all of the hydrogen atoms have formal charges of
zero. Notice that, as you would expect, the sum of the formal charges of all the atoms in the ion equals the total charge on the ion - this
will always be true for every example you encounter, and is a good way to check to make sure you are figuring individual formal
charges correctly.
An abbreviated formula for determining formal charges can be expressed as follows:
formal charge = (# valence electrons) - (# non-bonding electrons) - ( ½ # bonding electrons)
When drawing structures, it is very important to show all non-zero formal charges, being clear about where the charges are located.
When all non-zero formal charges are shown in the structure, the overall charge on an ion does not need to be indicated - that
information is obvious from the sum of the formal charges.
At this point, thinking back to what you learned in general chemistry, you are probably asking "What about dipoles? Doesn’t an
oxygen atom in an O-H bond ‘own’ more of the electron density than the hydrogen, because of its greater electronegativity?" You are
absolutely correct, and we will be reviewing the concept of dipoles later on. For the purpose of calculating formal charges, however,
dipoles don’t matter - we always consider the two electrons in a bond to be shared equally, even if that is not an accurate reflection of
chemical reality. Formal charges are just that - a formality, a method of electron book-keeping that is tied into the Lewis system for
drawing the structures of organic compounds and ions. Later, however, we will see how the concept can help us to visualize how
organic molecules react.

EXERCISE 1.5.4
Label all non-zero formal charges on the molecules/ions below. All atoms have a full octet of electrons (lone pairs are not shown).

Answer:

1.6.6 Updated 7/7/2019

HYBRIDIZATION OF ATOMIC ORBITALS AND THE SHAPE OF MOLECULES
If the four hydrogen atoms in a methane molecule, CH4, were bound to the three 2p orbitals and the 2s orbital of the carbon atom, the
H-C-H bond angles would be 90º for 3 of the hydrogen atoms and the 4th hydrogen atom would be at 135º from the others.
Experimental evidence has shown that the bond angles in methane are not arranged that way but are 109.5º giving the overall shape of
a tetrahedron. The tetrahedral structure makes much more sense in that hydrogen atoms would naturally repel each other due to their
negative electron clouds and form this shape. If you think electron-electron repulsion isn't significant, try walking through a wall!
There is plenty of space for your nuclei to pass through the nuclei of the wall material but ouch, it just doesn't work that way.
Experimental evidence has also shown that the H-N-H bond angles in ammonia (NH3) are 107º and the H-O-H bond angles in water
are 105º. It is clear from these bond angles that the non-bonding pairs of electrons occupy a reasonable amount of space and are
pushing the hydrogen atoms closer together compared to the angles found in methane.
The valence shell electron-pair repulsion model (VSEPR) was devised to account for these molecular shapes. In this model, atoms and
pairs of electrons will be arranged to minimize the repulsion of these atoms and pairs of electrons. Since the non-bonded electron pairs
are held somewhat closer to the nucleus than the attached hydrogen atoms, they tend to crowd the hydrogen atoms. Thus ammonia
exists as a distorted tetrahedron (trigonal pyramidal) rather than a trigonal plane and water also exists as a distorted tetrahedron (bent)
rather than a linear molecule with the hydrogen atoms at a 180º bond angle.
This concept proposes that since the attached groups are not at the angles of the p orbitals and their atomic orbitals would not have
maximum overlap (to form strong bonds) the s and p orbitals will be hybridized to match the bond angles of the attached groups.
The number of these new hybrid orbitals must be equal to the numbers of atoms and non-bonded electron pairs surrounding
the central atom!

This valence shell repulsion model can be illustrated at home with a very fun experiment!
EXAMPLE 1.5.5: METHANE
In the case of methane, the three 2p orbitals of the carbon atom are combined with its 2s orbital to form four new orbitals called sp3
hybrid orbitals. The name is simply a tally of all the orbitals that were blended together to form these new hybrid orbitals. Four
hybrid orbitals were required since there are four atoms attached to the central carbon atom. These new orbitals will have an energy
slightly above the 2s orbital and below the 2p orbitals as shown in the following illustration. Notice that no change occurred with
the 1s orbital.

These hybrid orbitals have 75% p-character and 25% s-character which gives them a shape that is shorter and fatter than a p-orbital.
The new shape looks a little like...

1.6.7 Updated 7/7/2019

A stick and wedge drawing of methane shows the tetrahedral angles. The wedge is coming out of the paper and the dashed line is
going behind the paper. The solid lines are in the plane of the paper.

A space-filling model of methane would look like...

EXAMPLE 1.5.6: AMMONIA

In the case of ammonia, the three 2p orbitals of the nitrogen atom are combined with the 2s orbital to form four sp3 hybrid orbitals.
We need a hybrid orbital for each atom and the pair of non-bonding electrons. Ammonia has three hydrogen atoms and one non-
bonded pair of electrons when we draw the electron-dot formula. In order to determine the hybridization of an atom, you must first
draw the electron-dot formula.

A stick and wedge drawing of ammonia showing the non-bonding electrons in a probability area for the hybrid orbital...

A space-filling model of ammonia would look like...(Note the non-bonded electron pair is not shown in this model.)

EXAMPLE 1.5.7: WATER

In the case of water, the three 2p orbitals of the oxygen atom are combined with the 2s orbital to form four sp3 hybrid orbitals. The
two non-bonded electron pairs will occupy hybrid orbitals. Again we need a hybrid orbital for each atom and each pair of non-
bonding electrons. Water has two hydrogen atoms and two non-bonded pairs of electrons when we draw the electron-dot formula.

1.6.8 Updated 7/7/2019

A stick and wedge drawing of water showing the non-bonding electron pairs in probability areas for the hybrid orbital...

A space-filling model of water would look like...(Note the non-bonded electron pairs are not shown in this model.)

EXAMPLE 1.5.8: BORON TRIFLUORIDE

Now let's look at something a bit different. In the boron trifluoride molecule, only three groups are arranged around the central
boron atom. In this case, the 2s orbital is combined with only two of the 2p orbitals (since we only need three hybrid orbitals for the
three groups...thinking of groups as atoms and non-bonding pairs) forming three hybrid orbitals called sp2 hybrid orbitals. The other
p-orbital remains non-hybridized and is at right angles to the trigonal planar arrangement of the hybrid orbitals. The trigonal planar
arrangement has bond angles of 120º.

In the following stick model, the empty p orbital is shown as the probability area...one end shaded blue and the other is white...there
are no electrons in this orbital!

A space-filling model of boron trifluoride would look like...

EXAMPLE 1.5.9: BERYLLIUM DICHLORIDE

Finally let's look at beryllium dichloride. Since only two groups are attached to beryllium, we only will have two hybrid orbitals. In
this case, the 2s orbital is combined with only one of the 2p orbitals to yield two sp hybrid orbitals. The two hybrid orbitals will be

1.6.9 Updated 7/7/2019

 arranged as far apart as possible from each other with the result being a linear arrangement. The two non-hybridized p-orbitals stay
in their respective positions (at right angles to each other) and perpendicular to the linear molecule.

In the following stick model, the empty p orbitals are shown as the probability areas...one green and one blue.

A space-filling model of beryllium dichloride would look like...

SUMMARY OF HYBRIDIZATION
In the following summary, groups are considered to be atoms and/or pairs of electrons and hybrid orbitals are the red lines and wedges.
When the octet of an element is exceeded, then hybridization will involve d-orbitals. Non-hybridized p-orbitals are shown as
probability areas in blue and green for sp hybridization and blue for sp2 hybridization. A single electron as found in a radical would
occupy an non-hybridized p-orbital.
Number of Groups Attached to a Description and 3-Dimensional Shape
Central Atom
Two Groups
sp

Three Groups
sp2

Four Groups
sp3

HYBRIDIZATION INVOLVING MULTIPLE BONDS

Only a maximum of two electrons can occupy any orbital whether it is an atomic orbital or a molecular orbital due to electron-electron
repulsion. When we draw a double or a triple-bond between two atoms, we imply that either four or six electrons are directly between
these two atoms. Since this is impossible, we must have these extra electrons off to the side in what we refer to as pi bonds. Therefore,
all multiple bonds are composed of two different kinds of molecular bonds called pi bonds and sigma bonds.
The sigma (σ) bond is defined as the linear overlap of atomic orbitals in which two electrons are directly between the two bonded
nuclei.
Pi (π) bonds are defined as the parallel overlap of p-orbitals. A double bond has one sigma bond and one pi bond. A triple bond thus
consists of a sigma bond and two pi bonds with the pi bonds in different planes.

EXAMPLE 1.5.10: ETHENE

In the ethene molecule, C2H4, both carbon atoms will be sp2 hybridized and have one unpaired electron in a non-hybridized p-
orbital.

1.6.10 Updated 7/7/2019

These p-orbitals will undergo parallel overlap and form one pi bond with bean-shaped probability areas above and below the plane
of the six atoms. This pair of bean-shaped probability areas constitutes one pi bond and the pair of electrons in this bond can be
found in either bean-shaped area.

The 3-dimensional model of ethene is planar with H-C-H and H-C-C bond angles of 120º...the pi bond is not shown in this picture.

EXAMPLE 1.5.11: ACETYLENE

Now let's look at acetylene, C2H2. Both carbon atoms will be sp hybridized and have one electron in each of two non-hybridized p-
orbitals.

These p orbitals will undergo parallel overlap to form two pi bonds at right angles to each other.

The 3-dimensional model of acetylene is therefore linear...the pi bonds are not shown in this picture.

THE RELATIONSHIP BETWEEN BOND ORDER AND BOND ENERGY

1.6.11 Updated 7/7/2019

Triple bonds between like atoms are shorter than double bonds, and because more energy is required to completely break all three
bonds than to completely break two, a triple bond is also stronger than a double bond. Similarly, double bonds between like atoms are
stronger and shorter than single bonds. Bonds of the same order between different atoms show a wide range of bond energies, however.
Table 1.5.1 lists the average values for some commonly encountered bonds. Although the values shown vary widely, we can observe
four trends:

Table 1.5.1: Average Bond Energies (kJ/mol) for Commonly Encountered Bonds at 273 K
Single Bonds Multiple Bonds
H–H 432 C–C 346 N–N ≈167 O–O ≈142 F–F 155 C=C 602

H–C 411 C–Si 318 N–O 201 O–F 190 F–Cl 249 C≡C 835

H–Si 318 C–N 305 N–F 283 O–Cl 218 F–Br 249 C=N 615

H–N 386 C–O 358 N–Cl 313 O–Br 201 F–I 278 C≡N 887

H–P ≈322 C–S 272 N–Br 243 O–I 201 Cl–Cl 240 C=O 749

H–O 459 C–F 485 P–P 201 S–S 226 Cl–Br 216 C≡O 1072

H–S 363 C–Cl 327 S–F 284 Cl–I 208 N=N 418

H–F 565 C–Br 285 S–Cl 255 Br–Br 190 N≡N 942

H–Cl 428 C–I 213 S–Br 218 Br–I 175 N=O 607

H–Br 362 Si–Si 222 I–I 149 O=O 494

H–I 295 Si–O 452 S=O 532

Source: Data from J. E. Huheey, E. A. Keiter, and R. L. Keiter, Inorganic Chemistry, 4th ed. (1993).

1. Bonds between hydrogen and atoms in the same column of the periodic table decrease in strength as we go down the column. Thus
an H–F bond is stronger than an H–I bond, H–C is stronger than H–Si, H–N is stronger than H–P, H–O is stronger than H–S, and so
forth. The reason for this is that the region of space in which electrons are shared between two atoms becomes proportionally
smaller as one of the atoms becomes larger (Figure 1.5.1a)
2. Bonds between like atoms usually become weaker as we go down a column (important exceptions are noted later). For example,
the C–C single bond is stronger than the Si–Si single bond, which is stronger than the Ge–Ge bond, and so forth. As two bonded
atoms become larger, the region between them occupied by bonding electrons becomes proportionally smaller. (Figure 1.5.1b)
Noteworthy exceptions are single bonds between the period 2 atoms of groups 15, 16, and 17 (i.e., N, O, F), which are unusually
weak compared with single bonds between their larger congeners. It is likely that the N–N, O–O, and F–F single bonds are weaker
than might be expected due to strong repulsive interactions between lone pairs of electrons on adjacent atoms. The trend in bond
energies for the halogens is therefore
Cl– Cl > Br– Br > F – F > I – I (1.6.1)

Similar effects are also seen for the O–O versus S–S and for N–N versus P–P single bonds.

Bonds between hydrogen and atoms in a given column in the periodic table are weaker
down the column; bonds between like atoms usually become weaker down a column.

3. Because elements in periods 3 and 4 rarely form multiple bonds with themselves, their multiple bond energies are not accurately
known. Nonetheless, they are presumed to be significantly weaker than multiple bonds between lighter atoms of the same families.
Compounds containing an Si=Si double bond, for example, have only recently been prepared, whereas compounds containing C=C
double bonds are one of the best-studied and most important classes of organic compounds.

1.6.12 Updated 7/7/2019

Figure 1.5.1 The Strength of Covalent Bonds Depends on the Overlap between the Valence Orbitals of the Bonded Atoms. The relative
sizes of the region of space in which electrons are shared between (a) a hydrogen atom and lighter (smaller) vs. heavier (larger) atoms
in the same periodic group; and (b) two lighter versus two heavier atoms in the same group. Although the absolute amount of shared
space increases in both cases on going from a light to a heavy atom, the amount of space relative to the size of the bonded atom
decreases; that is, the percentage of total orbital volume decreases with increasing size. Hence the strength of the bond decreases.
4. Multiple bonds between carbon, oxygen, or nitrogen and a period 3 element such as phosphorus or sulfur tend to be unusually
strong. In fact, multiple bonds of this type dominate the chemistry of the period 3 elements of groups 15 and 16. Multiple bonds to
phosphorus or sulfur occur as a result of d-orbital interactions, as we discussed for the SO42− ion in Section 8.6. In contrast, silicon
in group 14 has little tendency to form discrete silicon–oxygen double bonds. Consequently, SiO2 has a three-dimensional network
structure in which each silicon atom forms four Si–O single bonds, which makes the physical and chemical properties of SiO2 very
different from those of CO2.

NOTE
Bond strengths increase as bond order increases, while bond distances decrease.
Table 1.5.2: Average bond energies:
Bond (kJ/mol)

C-F 485

C-Cl 328

C-Br 276

C-I 240

C-C 348

C-N 293

C-O 358

C-F 485

C-C 348

C=C 614

C=C 839

EXERCISES
QUESTIONS
Q1.5.1
Draw an energy diagram for energy vs. intermolecular distance for a fluorine molecule (F2)
and describe the regions of the graph.
SOLUTIONS
S1.5.1

1.6.13 Updated 7/7/2019

A - Repulsive Forces are present, p-orbitals are too close together
B - Optimal distance between the two p-orbitals to have a bond (the bond length)
C - Cannot form a bond, orbitals are too far away

CONTRIBUTORS
Dr. Dietmar Kennepohl FCIC (Professor of Chemistry, Athabasca University)
Richard Banks (Boise State University)

1.6.14 Updated 7/7/2019

1.7: SP³ HYBRID ORBITALS AND THE STRUCTURE OF METHANE
OBJECTIVE
After completing this section, you should be able to describe the structure of methane in terms of the sp3 hybridization of the central
carbon atom.

KEY TERMS
Make certain that you can define, and use in context, the key terms below.
bond angle
hybridization
sp3 hybrid

STUDY NOTES
The tetrahedral shape is a very important one in organic chemistry, as it is the basic shape of all compounds in which a carbon atom
is bonded to four other atoms. Note that the tetrahedral bond angle of H − C − H is 109.5°.

BONDING IN METHANE, CH4

We are starting with methane because it is the simplest case which illustrates the sort of processes involved. You might remember that
the bonding picture of methane looks like this.

There is a serious mismatch between this structure and the modern electronic structure of carbon, 1s22s22px12py1. The modern
structure shows that there are only 2 unpaired electrons to share with hydrogens, instead of the 4 which the bonding picture requires.

You can see this more readily using the electrons-in-boxes notation. Only the 2nd level electrons are shown. The 1s2 electrons are too
deep inside the atom to be involved in bonding. The only electrons directly available for sharing are the 2p electrons. Why then isn't
methane CH2?

PROMOTION OF AN ELECTRON
When bonds are formed, energy is released and the system becomes more stable. If carbon forms 4 bonds rather than 2, twice as much
energy is released and so the resulting molecule becomes even more stable. There is only a small energy gap between the 2s and 2p
orbitals, and so it pays the carbon to provide a small amount of energy to promote an electron from the 2s to the empty 2p to give 4
unpaired electrons. The extra energy released when the bonds form more than compensates for the initial input.

The carbon atom is now said to be in an excited state. Now that we've got 4 unpaired electrons ready for bonding, another problem
arises. In methane all the carbon-hydrogen bonds are identical, but our electrons are in two different kinds of orbitals. You aren't going
to get four identical bonds unless you start from four identical orbitals.

HYBRIDIZATION

1.7.1 Updated 7/7/2019

The electrons rearrange themselves again in a process called hybridization. This reorganizes the electrons into four identical hybrid
orbitals called sp3 hybrids (because they are made from one s orbital and three p orbitals). You should read "sp3" as "s p three" - not as
"s p cubed".

sp3 hybrid orbitals look a bit like half a p orbital, and they arrange themselves in space so that they are as far apart as possible. You can
picture the nucleus as being at the center of a tetrahedron (a triangularly based pyramid) with the orbitals pointing to the corners. For
clarity, the nucleus is drawn far larger than it really is.
WHAT HAPPENS WHEN THE BONDS ARE FORMED?
Remember that hydrogen's electron is in a 1s orbital - a spherically symmetric region of space surrounding the nucleus where there is
some fixed chance (say 95%) of finding the electron. When a covalent bond is formed, the atomic orbitals (the orbitals in the individual
atoms) merge to produce a new molecular orbital which contains the electron pair which creates the bond.

Four molecular orbitals are formed, looking rather like the original sp3 hybrids, but with a hydrogen nucleus embedded in each lobe.
Each orbital holds the 2 electrons that we've previously drawn as a dot and a cross. The principles involved - promotion of electrons if
necessary, then hybridization, followed by the formation of molecular orbitals - can be applied to any covalently-bound molecule.

CONTRIBUTORS
Dr. Dietmar Kennepohl FCIC (Professor of Chemistry, Athabasca University)
Prof. Steven Farmer (Sonoma State University)
Organic Chemistry With a Biological Emphasis by Tim Soderberg (University of Minnesota, Morris)

1.7.2 Updated 7/7/2019

1.8: SP³ HYBRID ORBITALS AND THE STRUCTURE OF ETHANE
OBJECTIVE
After completing this section, you should be able to describe the structure of ethane in terms of the sp3 hybridization of the two
carbon atoms present in the molecule ethane.

In the ethane molecule, the bonding picture according to valence orbital theory is very similar to that of methane. Both carbons are sp3-
hybridized, meaning that both have four bonds arranged with tetrahedral geometry. The carbon-carbon bond, with a bond length of
1.54 Å, is formed by overlap of one sp3 orbital from each of the carbons, while the six carbon-hydrogen bonds are formed from
overlaps between the remaining sp3 orbitals on the two carbons and the 1s orbitals of hydrogen atoms. All of these are sigma bonds.

Because they are formed from the end-on-end overlap of two orbitals, sigma bonds are free to rotate. This means, in the case of ethane
molecule, that the two methyl (CH3) groups can be pictured as two wheels on a hub, each one able to rotate freely with respect to the
other.

In chapter 3 we will learn more about the implications of rotational freedom in sigma bonds, when we discuss the ‘conformation’ of
organic molecules.
The sp3 bonding picture is also used to described the bonding in amines, including ammonia, the simplest amine. Just like the carbon
atom in methane, the central nitrogen in ammonia is sp3-hybridized. With nitrogen, however, there are five rather than four valence
electrons to account for, meaning that three of the four hybrid orbitals are half-filled and available for bonding, while the fourth is fully
occupied by a non-bonding pair of electrons.
C2H4, also known as ethylene or ethene, is a gaseous material created synthetically through steam cracking. In nature, it is released in
trace amounts by plants to signal their fruits to ripen. Ethene consists of two sp2-hybridized carbon atoms, which are sigma bonded to
each other and to two hydrogen atoms each. The remaining non-hybridized p orbitals on each carbon overlap to form a pi bond, which
gives ethene its reactivity.

EXERCISE
QUESTIONS
Q1.7.1
Draw pentane, CH3CH2CH2CH2CH3, predict the bond angles within this molecule.
SOLUTIONS
S1.7.1

All the bond angles will be the same size.

CONTRIBUTORS
Dr. Dietmar Kennepohl FCIC (Professor of Chemistry, Athabasca University)

1.8.1 Updated 7/7/2019

Prof. Steven Farmer (Sonoma State University)
William Reusch, Professor Emeritus (Michigan State U.), Virtual Textbook of Organic Chemistry
Organic Chemistry With a Biological Emphasis by Tim Soderberg (University of Minnesota, Morris)

1.8.2 Updated 7/7/2019

1.9: SP² HYBRID ORBITALS AND THE STRUCTURE OF ETHYLENE
OBJECTIVES
After completing this section, you should be able to
1. account for the formation of carbon-carbon double bonds using the concept of sp2 hybridization.
2. describe a carbon-carbon double bond as consisting of one σ bond and one π bond.
3. explain the difference between a σ bond and a π bond in terms of the way in which p orbitals overlap.

KEY TERMS
Make certain that you can define, and use in context, the key terms below.
pi (π) bond
sp2 hybrid

BONDING IN ETHYLENE
A key component of using Valence Bond Theory correctly is being able to draw the Lewis dot diagram correctly. Ethylene, commonly
known as ethene, has a double bond between the carbons and single bonds between each hydrogen and carbon: each bond is
represented by a pair of dots, which represent electrons. Each carbon requires a full octet and each hydrogen requires a pair of
electrons. The correct Lewis structure for ethylene is shown below:

In the molecule ethene, both carbon atoms will be sp2 hybridized and have one unpaired electron in a non-hybridized p orbital.

These p-orbitals will undergo parallel overlap and form one sigma bond with bean-shaped probability areas above and below the plane
of the six atoms. This pair of bean-shaped probability areas constitutes one pi bond and the pair of electrons in this bond can be found
in either bean-shaped area.

The 3-dimensional model of ethene is therefore planar with H-C-H and H-C-C bond angles of 120º. Thepi bond is not shown in this
picture.

1.9.1 Updated 7/7/2019

Valence Shell Electron Pair Repulsion (VSEPR) Theory is used to predict the bond angles and spatial positions of the carbon and
hydrogen atoms of ethene and to determine the bond order of the carbon atoms (the number of bonds formed between them). Each
carbon atom is of the general arrangement AX3, where A is the central atom surrounded by three other atoms (denoted by X);
compounds of this form adopt trigonal planar geometry, forming 120 degree bond angles. In order for the non-hybridized p orbitals to
successfully overlap, the CH2 must be coplanar: therefore, C2H4 is a planar molecule and each bond angle is about 120 degrees. The
diagram below shows the bond lengths and hydrogen-carbon-carbon bond angles of ethene:

According to valence bond theory, two atoms form a covalent bond through the overlap of individual half-filled valence atomic
orbitals, each containing one unpaired electron. In ethene, each hydrogen atom has one unpaired electron and each carbon is sp2
hybridized with one electron each sp2 orbital. The fourth electron is in the p orbital that will form the pi bond. The bond order for
ethene is simply the number of bonds between each atom: the carbon-carbon bond has a bond order of two, and each carbon-hydrogen
bond has a bond order of one.

EXERCISE
QUESTIONS
Q1.8.1
Consider the following molecule:

At each atom, what is the hybridization and the bond angle? At atom A draw the molecular orbital.
SOLUTIONS
S1.8.1
A - sp2, 120°
B - sp3, 109°
C - sp2, 120° (with the lone pairs present)
D - sp3, 109°

CONTRIBUTORS
Dr. Dietmar Kennepohl FCIC (Professor of Chemistry, Athabasca University)

1.9.2 Updated 7/7/2019

Prof. Steven Farmer (Sonoma State University)
William Reusch, Professor Emeritus (Michigan State U.), Virtual Textbook of Organic Chemistry
Organic Chemistry With a Biological Emphasis by Tim Soderberg (University of Minnesota, Morris)

1.9.3 Updated 7/7/2019

1.10: SP HYBRID ORBITALS AND THE STRUCTURE OF ACETYLENE
OBJECTIVES
After completing this section, you should be able to
1. use the concept of sp hybridization to account for the formation of carbon-carbon triple bonds, and describe a carbon-carbon
triple bond as consisting of one σ bond and two π bonds.
2. list the approximate bond lengths associated with typical carbon-carbon single bonds, double bonds and triple bonds. [You may
need to review Sections 1.7 and 1.8.]
3. list the approximate bond angles associated with sp3-, sp2- and sp‑hybridized carbon atoms and predict the bond angles to be
expected in given organic compounds. [If necessary, review Sections 1.6, 1.7 and 1.8.]
4. account for the differences in bond length, bond strength and bond angles found in compounds containing sp3-, sp2- and
sp‑hybridized carbon atoms, such as ethane, ethylene and acetylene.

KEY TERMS
Make certain that you can define, and use in context, the key term below.
sp hybrid orbital

STUDY NOTES
The bond angles associated with sp3-, sp2- and sp‑hybridized carbon atoms are approximately 109.5°, 120° and 180°, respectively.

BONDING IN ACETYLENE
Finally, the hybrid orbital concept applies well to triple-bonded groups, such as alkynes and nitriles. Consider, for example, the
structure of ethyne (another common name is acetylene), the simplest alkyne.

This molecule is linear: all four atoms lie in a straight line. The carbon-carbon triple bond is only 1.20Å long. In the hybrid orbital
picture of acetylene, both carbons are sp-hybridized. In an sp-hybridized carbon, the 2s orbital combines with the 2px orbital to form
two sp hybrid orbitals that are oriented at an angle of 180°with respect to each other (eg. along the x axis). The 2py and 2pz orbitals
remain non-hybridized, and are oriented perpendicularly along the y and z axes, respectively.

The C-C sigma bond is formed by the overlap of one sp orbital from each of the carbons, while the two C-H sigma bonds are formed
by the overlap of the second sp orbital on each carbon with a 1s orbital on a hydrogen. Each carbon atom still has two half-filled 2py
and 2pz orbitals, which are perpendicular both to each other and to the line formed by the sigma bonds. These two perpendicular pairs
of p orbitals form two pi bonds between the carbons, resulting in a triple bond overall (one sigma bond plus two pi bonds).

1.10.1 Updated 7/7/2019

The hybrid orbital concept nicely explains another experimental observation: single bonds adjacent to double and triple bonds are
progressively shorter and stronger than ‘normal’ single bonds, such as the one in a simple alkane. The carbon-carbon bond in ethane
(structure A below) results from the overlap of two sp3 orbitals.

In alkene B, however, the carbon-carbon single bond is the result of overlap between an sp2 orbital and an sp3 orbital, while in alkyne
C the carbon-carbon single bond is the result of overlap between an sp orbital and an sp3 orbital. These are all single bonds, but the
single bond in molecule C is shorter and stronger than the one in B, which is in turn shorter and stronger than the one in A.
The explanation here is relatively straightforward. An sp orbital is composed of one s orbital and one p orbital, and thus it has 50% s
character and 50% p character. sp2 orbitals, by comparison, have 33% s character and 67% p character, while sp3 orbitals have 25% s
character and 75% p character. Because of their spherical shape, 2s orbitals are smaller, and hold electrons closer and ‘tighter’ to the
nucleus, compared to 2p orbitals. Consequently, bonds involving sp + sp3 overlap (as in alkyne C) are shorter and stronger than bonds
involving sp2 + sp3 overlap (as in alkene B). Bonds involving sp3-sp3overlap (as in alkane A) are the longest and weakest of the group,
because of the 75% ‘p’ character of the hybrids.

COMPARISON OF C-C BONDS ETHANE, ETHYLENE, AND ACETYLENE

Molecule Bond Bond Strength (kJ/mol) Bond Length (pm)
Ethane, CH3CH3 (sp3) C-C (sp3) 376 154
Ethylene, H2C=CH2 (sp2) C=C (sp2) 728 134
Acetylene, 965 120
(sp) (sp)

Notice that as the bond order increases the bond length decreases and the bond strength increases.

EXERCISES
QUESTIONS
Q1.9.1
1-Cyclohexyne is a very strained molecule. By looking at the molecule explain why there is
such a intermolecular strain using the knowledge of hybridization and bond angles.

SOLUTIONS
S1.9.1
The alkyne is a sp hybridized orbital. By looking at a sp orbital, we can see that the bond angle is 180°, but in cyclohexane the regular
angles would be 109.5°. Therefore the molecule would be strained to force the 180° to be a 109°.

CONTRIBUTORS
Dr. Dietmar Kennepohl FCIC (Professor of Chemistry, Athabasca University)
Prof. Steven Farmer (Sonoma State University)
William Reusch, Professor Emeritus (Michigan State U.), Virtual Textbook of Organic Chemistry

1.10.2 Updated 7/7/2019

Organic Chemistry With a Biological Emphasis by Tim Soderberg (University of Minnesota, Morris)

1.10.3 Updated 7/7/2019

1.11: HYBRIDIZATION OF NITROGEN, OXYGEN, PHOSPHORUS AND
SULFUR
OBJECTIVE
After completing this section, you should be able to apply the concept of hybridization of atoms such as N, O, P and S to explain
the structures of simple species containing these atoms.

KEY TERMS
Make certain that you can define, and use in context, the key term below.
lone pair electrons

STUDY NOTES
Nitrogen is frequently found in organic compounds. As with carbon atoms, nitrogen atoms can be sp3-, sp2- or sp‑hybridized.
Note that, in this course, the term “lone pair” is used to describe an unshared pair of electrons.

The valence-bond concept of orbital hybridization can be extrapolated to other atoms including nitrogen, oxygen, phosphorus, and
sulfur. In other compounds, covalent bonds that are formed can be described using hybrid orbitals.

METHYL AMINE
The nitrogen is sp3 hybridized which means that it has four sp3 hybrid orbitals. Two of the sp3 hybridized orbitals overlap with s
orbitals from hydrogens to form the two N-H sigma bonds. One of the sp3 hybridized orbitals overlap with an sp3 hybridized orbital
from carbon to form the C-N sigma bond. The lone pair electrons on the nitrogen are contained in the last sp3 hybridized orbital. Due
to the sp3 hybridization the nitrogen has a tetrahedral geometry. However, the H-N-H and H-N-C bonds angles are less than the typical
109.5o due to compression by the lone pair electrons.

Methylamine

METHANOL
The oxygen is sp3 hybridized which means that it has four sp3 hybrid orbitals. One of the sp3 hybridized orbitals overlap with s orbitals
from a hydrogen to form the O-H sigma bonds. One of the sp3 hybridized orbitals overlap with an sp3 hybridized orbital from carbon to
form the C-O sigma bond. Both the sets of lone pair electrons on the oxygen are contained in the remaining sp3 hybridized orbital. Due
to the sp3 hybridization the oxygen has a tetrahedral geometry. However, the H-O-C bond angles are less than the typical 109.5o due to
compression by the lone pair electrons.

Methanol

METHYL PHOSPHATE
Phosphorus can have have expanded octets because it is in the n = 3 row. Typically, phosphorus forms five covalent bonds. In
biological molecules, phosphorus is usually found in organophosphates. Organophosphates are made up of a phosphorus atom bonded
to four oxygens, with one of the oxygens also bonded to a carbon. In methyl phosphate, the phosphorus is sp3 hybridized and the O-P-
O bond angle varies from 110 ° to 112o.

1.11.1 Updated 7/7/2019

 Methyl Phosphate

METHANETHIOL & DIMETHYL SULFIDE

In biological system, sulfur is typically found in molecules called thiols or sulfides. In a thiol, the sulfur atom is bonded to one
hydrogen and one carbon and is analogous to an alcohol O-H bond. In a sulfide, the sulfur is bonded to two carbons. In both cases the
sulfur is sp3 hybridized and the bond angles are much less than the typical 109.5o.

Methanethiol

Dimethyl sulfide

EXERCISES
QUESTIONS
Q1.10.1
Identify geometry and lone pairs on each heteroatom of the molecules given.

SOLUTIONS
S1.10.1
Diethyl ether would have two lone pairs of electrons and would have a bent geometry around the oxygen.
Dimethyl amine would have one lone pair and would show a pyramidal geometry around the nitrogen.

CONTRIBUTORS
Dr. Dietmar Kennepohl FCIC (Professor of Chemistry, Athabasca University)
Prof. Steven Farmer (Sonoma State University)

1.11.2 Updated 7/7/2019

1.12: THE NATURE OF CHEMICAL BONDS: MOLECULAR ORBITAL THEORY
OBJECTIVES
After completing this section, you should be able to
1. describe the formation of covalent bonds in terms of molecular orbitals.
2. account for differences in bond length and strength in terms of the efficiency with which atomic orbitals overlap.
3. draw simple molecular orbital diagrams (e.g., for the H2 molecule) showing the formation of bonding and anti-bonding orbitals.

KEY TERMS
Make certain that you can define, and use in context, the key terms below.
anti-bonding molecular orbital
bonding molecular orbital
molecular orbital (MO) theory

As we have seen, valence bond theory does a remarkably good job of explaining the bonding geometry and properties of many organic
compounds. There are some areas, however, where the valence bond theory falls short. It fails to adequately account, for example, for
some interesting properties of compounds that contain alternating double and single bonds. In order to understand these properties, we
need to think about chemical bonding in a new way, using the ideas of molecular orbital (MO) theory.

ANOTHER LOOK AT THE H2 MOLECULE: BONDING AND ANTI-BONDING SIGMA MOLECULAR

ORBITALS
Let’s consider again the simplest possible covalent bond: the one in molecular hydrogen (H2). When we described the hydrogen
molecule using valence bond theory, we said that the two 1s orbitals from each atom overlap, allowing the two electrons to be shared
and thus forming a covalent bond. In molecular orbital theory, we make a further statement: we say that the two atomic 1s orbitals
don’t just overlap, they actually combine to form two completely new orbitals. These two new orbitals, instead of describing the likely
location of an electron around a single nucleus, describe the location of an electron pair around two or more nuclei. The bonding in H2,
then, is due to the formation of a new molecular orbital (MO), in which a pair of electrons is delocalized around two hydrogen nuclei.
An important principle of quantum mechanical theory is that when orbitals combine, the number of orbitals before the combination
takes place must equal the number of new orbitals that result – orbitals don’t just disappear! We saw this previously when we discussed
hybrid orbitals: one s and three p orbitals make four sp3 hybrids. When two atomic 1s orbitals combine in the formation of H2, the
result is two molecular orbitals called sigma (σ) orbitals. According to MO theory, the first sigma orbital is lower in energy than either
of the two isolated atomic 1s orbitals – thus this sigma orbital is referred to as a bonding molecular orbital. The second, sigma-star
(σ*) orbital is higher in energy than the two atomic 1s orbitals, and is referred to as an anti-bonding molecular orbital. In MO
theory, a star (*) sign always indicates an anti-bonding orbital.

Following the aufbau ('building up') principle, we place the two electrons in the H2 molecule in the lowest energy molecular orbital,
which is the (bonding) sigma orbital.
The bonding sigma orbital, which holds both electrons in the ground state of the molecule, is egg-shaped, encompassing the two nuclei,
and with the highest likelihood of electrons being in the area between the two nuclei. The high-energy, anti-bonding sigma-star orbital
can be visualized as a pair of droplets, with areas of higher electron density near each nucleus and a ‘node’, (area of zero electron
density) midway between the two nuclei.
Remember that we are thinking here about electron behavior as wave behavior. When two separate waves combine, they can do so
with what is called constructive interference, where the two amplitudes reinforce one another, or destructive interference, where the
two amplitudes cancel one another out. Bonding MO’s are the consequence of constructive interference between two atomic orbitals
which results in an attractive interaction and an increase in electron density between the nuclei. Anti-bonding MO’s are the

1.12.1 Updated 7/7/2019

consequence of destructive interference which results in a repulsive interaction and a ‘canceling out’ of electron density between the
nuclei (in other words, a node).

MO THEORY AND PI BONDS - CONJUGATION

The advantage of MO theory becomes more apparent when we think about pi bonds, especially in those situations where two or more
pi bonds are able to interact with one another. Let’s first consider the pi bond in ethene from an MO theory standpoint (in this example
we will be disregarding the various sigma bonds, and thinking only about the pi bond). According to MO theory, the two atomic 2pz
orbitals combine to form two pi (π) molecular orbitals, one a low-energy π bonding orbital and one a high-energy π-star (π*) anti-
bonding molecular orbital. These are sometimes denoted, in MO diagrams like the one below, with the Greek letter psi (Ψ) instead of
π.

In the bonding Ψ1 orbital, the two shaded lobes of the 2pz orbitals interact constructively with each other, as do the two unshaded lobes
(remember, the shading choice represents mathematical (+) and (-) signs for the wavefunction). Therefore, there is increased electron
density between the nuclei in the molecular orbital – this is why it is a bonding orbital.
In the higher-energy anti-bonding Ψ2* orbital, the shaded lobe of one 2pz orbital interacts destructively with the unshaded lobe of the
second 2pz orbital, leading to a node between the two nuclei and overall repulsion.
By the aufbau principle, the two electrons from the two atomic orbitals will be paired in the lower-energy Ψ1orbital when the molecule
is in the ground state.

EXERCISES
1. Draw a simple molecular orbital diagram for each of the following molecules
a. nitrogen, N2.
b. oxygen, O2.

ANSWERS:
 Answers
CONTRIBUTORS
Dr. Dietmar Kennepohl FCIC (Professor of Chemistry, Athabasca University)
Prof. Steven Farmer (Sonoma State University)
Organic Chemistry With a Biological Emphasis by Tim Soderberg (University of Minnesota, Morris)

1.12.2 Updated 7/7/2019

1.13: DRAWING CHEMICAL STRUCTURES
OBJECTIVES
After completing this section, you should be able to
1. propose one or more acceptable Kekulé structures (structural formulas) for any given molecular formula
2. write the molecular formula of a compound, given its Kekulé structure.
3. draw the shorthand structure of a compound, given its Kekulé structure.
4. interpret shorthand structures and convert them to Kekulé structures.
5. write the molecular formula of a compound, given its shorthand structure.

STUDY NOTES
When drawing the structure of a neutral organic compound, you will find it helpful to remember that
each carbon atom has four bonds.
each nitrogen atom has three bonds.
each oxygen atom has two bonds.
each hydrogen atom has one bond.

It is necessary to draw structural formulas for organic compounds because in most cases a molecular formula does not uniquely
represent a single compound. Different compounds having the same molecular formula are called isomers, and the prevalence of
organic isomers reflects the extraordinary versatility of carbon in forming strong bonds to itself and to other elements. When the group
of atoms that make up the molecules of different isomers are bonded together in fundamentally different ways, we refer to such
compounds as constitutional isomers. There are seven constitutional isomers of C4H10O, and structural formulas for these are drawn
in the following table. These formulas represent all known and possible C4H10O compounds, and display a common structural feature.
There are no double or triple bonds and no rings in any of these structures.

1.13.1 Updated 7/7/2019

 Table 1.13.1: Structural Formulas for C4H10O isomers
Kekulé Formula Condensed Formula Shorthand Formula

Simplification of structural formulas may be achieved without any loss of the information they convey. In condensed structural
formulas the bonds to each carbon are omitted, but each distinct structural unit (group) is written with subscript numbers designating
multiple substituents, including the hydrogens. Shorthand (line) formulas omit the symbols for carbon and hydrogen entirely (unless
the hydrogen is bonded to an atom other than carbon). Each straight line segment represents a bond, the ends and intersections of the
lines are carbon atoms, and the correct number of hydrogens is calculated from the tetravalency of carbon. Non-bonding valence shell
electrons are omitted in these formulas.
Developing the ability to visualize a three-dimensional structure from two-dimensional formulas requires practice, and in most cases
the aid of molecular models. As noted earlier, many kinds of model kits are available to students and professional chemists, and the
beginning student is encouraged to obtain one.

KEKULÉ FORMULA

1.13.2 Updated 7/7/2019

A Kekulé Formula or structural formula displays the atoms of the molecule in the order they are bonded. It also depicts how the atoms
are bonded to one another, for example single, double, and triple covalent bond. Covalent bonds are shown using lines. The number of
dashes indicate whether the bond is a single, double, or triple covalent bond. Structural formulas are helpful because they explain the
properties and structure of the compound which empirical and molecular formulas cannot always represent.

Figure 1.13.1: Kekulé Formula for Ethanol

CONDENSED FORMULA
Condensed structural formulas show the order of atoms like a structural formula but are written in a single line to save space and make
it more convenient and faster to write out. Condensed structural formulas are also helpful when showing that a group of atoms is
connected to a single atom in a compound. When this happens, parenthesis are used around the group of atoms to show they are
together.
Ex. Condensed Structural Formula for Ethanol: CH3CH2OH (Molecular Formula for Ethanol C2H6O).

SHORTHAND FORMULA
Because organic compounds can be complex at times, line-angle formulas are used to write carbon and hydrogen atoms more
efficiently by replacing the letters with lines. A carbon atom is present wherever a line intersects another line. Hydrogen atoms are then
assumed to complete each of carbon's four bonds. All other atoms that are connected to carbon atoms are written out. Line angle
formulas help show structure and order of the atoms in a compound making the advantages and disadvantages similar to structural
formulas.

Figure 1.13.2: Shorthand Formula for Ethanol

EXERCISES
Write down the molecular formula for each of the compounds shown here.

ANSWERS:
A. C7H7N
B. C5H10
C. C5H4O
D. C5H6Br2
QUESTIONS
Q1.12.1
Below is the molecule for caffeine. Give the molecular formula for it.

1.13.3 Updated 7/7/2019

SOLUTIONS
S1.12.1
C8H10O2N4

CONTRIBUTORS
Dr. Dietmar Kennepohl FCIC (Professor of Chemistry, Athabasca University)
Prof. Steven Farmer (Sonoma State University)
William Reusch, Professor Emeritus (Michigan State U.), Virtual Textbook of Organic Chemistry
Organic Chemistry With a Biological Emphasis by Tim Soderberg (University of Minnesota, Morris)

1.13.4 Updated 7/7/2019

1.14: STRUCTURE AND BONDING (SUMMARY)
CONCEPTS & VOCABULARY
1.0: Prelude to Structure and Bonding
Organic compounds contain carbon atoms bonded hydrogen and other carbon atoms.
Organic chemistry studies the properties and reactions of organic compounds.
1.1: Atomic Structure: The Nucleus
Atoms are comprised of protons, neutrons and electrons. Protons and neutrons are found in the nucleus of the atom, while
electrons are found in the electron cloud around the nucleus. The relative electrical charge of a proton is +1, a neutron has no
charge, and an electron’s relative charge is -1.
The number of protons in an atom’s nucleus is called the atomic number, Z.
The mass number, A, is the sum of the number of protons and the number of neutrons in a nucleus.
The type of element an atom represents is defined by the atomic number, Z in the atom. All atoms of one specific element have the
same number of protons (Z).
Atoms that have the same atomic number (Z), but different mass numbers (A) are called isotopes.
1.2: Atomic Structure: Orbitals
An atomic orbital is the probability description of where an electron can be found. The four basic types of orbitals are designated
as s, p, d, and f.
1.3: Atomic Structure: Electron Configurations
The order in which electrons are placed in atomic orbitals is called the electron configuration and is governed by the aufbau
principle.
Electrons in the outermost shell of an atom are called valence electrons. The number of valence electrons in any atom is related to
its position in the periodic table. Elements in the same periodic group have the same number of valence electrons.
1.4: Development of Chemical Bonding Theory
Lewis Dot Symbols are a way of indicating the number of valence electrons in an atom. They are useful for predicting the number
and types of covalent bonds within organic molecules.
The molecular shape of molecules is predicted by Valence Shell Electron Pair Repulsion (VSEPR) theory. The shapes of common
organic molecules are based on tetrahedral, trigonal planar or linear arrangements of electron groups.
1.5: The Nature of Chemical Bonds: Valence Bond Theory
Covalent bonds form as valence electrons are shared between two atoms.
Lewis Structures and structural formulas are common ways of showing the covalent bonding in organic molecules.
Formal charge describes the changes in the number of valence electrons as an atom becomes bonded into a molecule. If the atom
has a net loss of valence electrons it will have a positive formal charge. If the atom has a net gain of valence electrons it will have a
negative formal charge.
Atomic orbitals often change as they overlap to form molecular orbitals. This process is known as orbital hybridization. The
common types of hybrid orbitals in organic molecules are sp3, sp2, and sp.
1.6: sp Hybrid Orbitals and the Structure of Methane
3

The four identical C-H single bonds in CH4 form as the result of sigma bond overlap between the sp3 hybrid orbitals of carbon and
the s orbital of each hydrogen.
1.7: sp Hybrid Orbitals and the Structure of Ethane
3

The C-C bond in C2H6 forms as the result of sigma bond overlap between a sp3 hybrid orbital on each carbon. and the s orbital of
each hydrogen. The six identical C-H single bonds in form as the result of sigma bond overlap between the sp3 hybrid orbitals of
carbon and the s orbital of each hydrogen.
1.8: sp Hybrid Orbitals and the Structure of Ethylene
2

The C=C bond in C2H4 forms as the result of both a sigma bond overlap between a sp2 hybrid orbital on each carbon and a pi bond
overlap of a p orbital on each carbon
1.9 sp Hybrid Orbitals and the Structure of Acetylene

1.14.1 Updated 7/7/2019

 The carbon-carbon triple bond in C2H4 forms as the result of one sigma bond overlap between a sp hybrid orbital on each carbon
and two pi bond overlaps of p orbitals on each carbon.
1.10: Hybridization of Nitrogen, Oxygen, Phosphorus and Sulfur
The atomic orbitals of nitrogen, oxygen, phosphorus and sulfur can hybridize in the same way as those of carbon.
1.11: The Nature of Chemical Bonds: Molecular Orbital Theory
Molecular Orbital theory (MO) is a more advanced bonding model than Valence Bond Theory, in which two atomic orbitals
overlap to form two molecular orbitals – a bonding MO and an anti-bonding MO.
1.12: Drawing Chemical Structures
Kekulé Formulas or structural formulas display the atoms of the molecule in the order they are bonded.
Condensed structural formulas show the order of atoms like a structural formula but are written in a single line to save space.
Skeleton formulas or Shorthand formulas or line-angle formulas are used to write carbon and hydrogen atoms more efficiently
by replacing the letters with lines.
Isomers have the same molecular formula, but different structural formulas

SKILLS TO MASTER
Skill 1.1 Determine the number of protons, neutrons, and electrons in a nuclide.
Skill 1.2 Write the electron configuration and orbital diagram for an atom.
Skill 1.3 Determine the number of valence electrons in an atom.
Skill 1.4 Draw the molecular formula, Lewis Dot Structure, structural formula, condensed structural formula, shorthand formula and
wedge-dash structure of simple organic molecules.
Skill 1.5 Use Lewis Dot structures to predict molecular shape, bond angle, hybridization.
Skill 1.6 Calculate formal charge on an atom in a molecule.
Skill 1.7 Determine the number of sigma and pi bonds in organic molecules.
Skill 1.8 Determine relative bond energy and bond length based on atoms involved in the bond and bond type.
Skill 1.9 Describe and draw the orbital overlap and types of bonding in simple organic molecules like methane, ethane, ethylene and
acetylene.
Skill 1.10 Describe the bonding in organic molecules using both the Valence Bond Theory and Molecular Orbital Theory.

MEMORIZATION TASKS (MT)

MT 1.1 Memorize the number of valence electrons in the atoms - C, H, N, O, and the halides.
MT 1.2 Memorize the number of bonds and lone pairs to atoms of carbon, hydrogen, oxygen and nitrogen that result in formal charges
of zero.

CONTRIBUTORS
Dr. Kelly Matthews (Professor of Chemistry, Harrisburg Area Community College)

1.14.2 Updated 7/7/2019

2: POLAR COVALENT BONDS; ACIDS AND BASES
This chapter provides a review of the more advanced material covered in a standard introductory chemistry course through a discussion
of the following topics: the drawing and interpretation of organic chemical structures. the use of ball-and-stick molecular models. the
concept of formal charge. the use of electronegativities to determine bond polarity, and the application of this knowledge to determining
whether a given molecule possesses a dipole moment. the Brønsted-Lowry and Lewis definition

2.1: POLAR COVALENT BONDS - ELECTRONEGATIVITY

Because the tendency of an element to gain or lose electrons is so important in determining its chemistry, various methods have been
developed to quantitatively describe this tendency. The most important method uses a measurement called electronegativity, defined as
the relative ability of an atom to attract electrons to itself in a chemical compound.

2.2: POLAR COVALENT BONDS - DIPOLE MOMENTS

Mathematically, dipole moments are vectors; they possess both a magnitude and a direction. The dipole moment of a molecule is
therefore the vector sum of the dipole moments of the individual bonds in the molecule. If the individual bond dipole moments cancel
one another, there is no net dipole moment.

2.3: FORMAL CHARGES

A formal charge is the charge assigned to an atom in a molecule, assuming that electrons in all chemical bonds are shared equally
between atoms, regardless of relative electronegativity.

2.4: RESONANCE
Resonance structures are a set of two or more Lewis Structures that collectively describe the electronic bonding a single polyatomic
species including fractional bonds and fractional charges. Resonance structure are capable of describing delocalized electrons that
cannot be expressed by a single Lewis formula with an integer number of covalent bonds.

2.5: RULES FOR RESONANCE FORMS

The above resonance structures show that the electrons are delocalized within the molecule and through this process the molecule gains
extra stability. Ozone with both of its opposite formal charges creates a neutral molecule and through resonance it is a stable molecule.
The extra electron that created the negative charge one terminal oxygen can be delocalized by resonance through the other terminal
oxygen.

2.6: DRAWING RESONANCE FORMS

Resonance structures are used when one Lewis structure for a single molecule cannot fully describe the bonding that takes place
between neighboring atoms relative to the empirical data for the actual bond lengths between those atoms. The net sum of valid
resonance structures is defined as a resonance hybrid, which represents the overall delocalization of electrons within the molecule. A
molecule that has several resonance structures is more stable than one with fewer.

2.7: ACIDS AND BASES - THE BRØNSTED-LOWRY DEFINITION

In 1923, chemists Johannes Brønsted and Martin Lowry independently developed definitions of acids and bases based on compounds
abilities to either donate or accept protons (H+ ions). Here, acids are defined as being able to donate protons in the form of hydrogen
ions; whereas bases are defined as being able to accept protons. This took the Arrhenius definition one step further as water is no longer
required to be present in the solution for acid and base reactions to occur.

2.8: ACID AND BASE STRENGTH

The relative acidity of different compounds or functional groups – in other words, their relative capacity to donate a proton to a common
base under identical conditions – is quantified by a number called the dissociation constant, abbreviated Ka. The common base chosen
for comparison is water.

2.9: PREDICTING ACID-BASE REACTIONS FROM PKA VALUES

2.10: ORGANIC ACIDS AND ORGANIC BASES
2.11: ACIDS AND BASES - THE LEWIS DEFINITION
A broader definition is provided by the Lewis theory of acids and bases, in which a Lewis acid is an electron-pair acceptor and a Lewis
base is an electron-pair donor. This definition covers Brønsted-Lowry proton transfer reactions, but also includes reactions in which no
proton transfer is involved.

2.12: MOLECULAR MODELS

2.13: POLAR COVALENT BONDS; ACIDS AND BASES (SUMMARY)

TOC.1 Updated 7/14/2019

2.1: POLAR COVALENT BONDS - ELECTRONEGATIVITY
OBJECTIVES
After completing this section, you should be able to
1. describe how differences in electronegativity give rise to bond polarity.
2. arrange a given series of the elements most often encountered in organic chemistry (C, H, O, N, S, P and the halogens) in order
of increasing or decreasing electronegativity, without referring to a table of electronegativities.
3. predict the partial positive and partial negative ends of a given bond formed between any two of the elements listed in Objective
2, above, without the use of a table of electronegativities or a periodic table.
4. predict the partial positive and partial negative ends of a given bond formed between any two elements not listed in Objective 2,
above, using a periodic table.

KEY TERMS
Make certain that you can define, and use in context, the key terms below.
electronegativity inductive effect
polar covalent bond

STUDY NOTES
Students often wonder why it is important to be able to tell whether a given bond is polar or not, and why they need to know which
atoms carry a partial positive charge and which a partial negative charge. Consider the chloromethane (CH3Cl) molecule. The
carbon atom is shown as carrying a partial positive charge. Now, recall that opposite charges attract. Thus, it seems reasonable that
the slightly positive carbon atom in chloromethane should be susceptible to attack by a negatively charged species, such as the
hydroxide ion, OH−. This theory is borne out in practice: hydroxide ions react with chloromethane by attacking the slightly positive
carbon atom in the latter. It is often possible to rationalize chemical reactions in this manner, and you will find the knowledge of
bond polarity indispensible when you start to write reaction mechanisms.
Note: Because of the small difference in electronegativity between carbon and hydrogen, the C-H bond is normally assumed to be
nonpolar.

ELECTRONEGATIVITY
The elements with the highest ionization energies are generally those with the most negative electron affinities, which are located
toward the upper right corner of the periodic table. Conversely, the elements with the lowest ionization energies are generally those
with the least negative electron affinities and are located in the lower left corner of the periodic table.
Because the tendency of an element to gain or lose electrons is so important in determining its chemistry, various methods have been
developed to quantitatively describe this tendency. The most important method uses a measurement called electronegativity
(represented by the Greek letter chi, χ, pronounced “ky” as in “sky”), which is defined as the relative ability of an atom to attract
electrons to itself in a chemical compound. Elements with high electronegativities tend to acquire electrons in chemical reactions and
are found in the upper right corner of the periodic table. Elements with low electronegativities tend to lose electrons in chemical
reactions and are found in the lower left corner of the periodic table.
Unlike ionization energy or electron affinity, the electronegativity of an atom is not a simple, fixed property that can be directly
measured in a single experiment. In fact, an atom’s electronegativity should depend to some extent on its chemical environment
because the properties of an atom are influenced by the neighboring atoms in a chemical compound. Nevertheless, when different
methods for measuring the electronegativity of an atom are compared, they all tend to assign similar relative values to a given element.
For example, all scales predict that fluorine has the highest electronegativity and cesium the lowest of the stable elements, which
suggests that all the methods are measuring the same fundamental property.

Electronegativity is de ned as the ability of an atom in a particular molecule to attract

electrons to itself. The larger the electronegativity value, the greater the attraction.

2.1.1 Updated 7/7/2019

Unfortunately there is no direct way of measuring electronegativity. Dipole-moment measurements tell us about the electrical behavior
of all electron pairs in the molecule, not just the bonding pair in which we are interested. Also, the polarity of a bond depends on
whether the bond is a single, double, or triple bond and on what the other atoms and electron pairs in a molecule are. Therefore the
dipole moment cannot tell us quantitatively the difference between the electronegativities of two bonded atoms. Various attempts have
been made over the years to derive a scale of electronegativities for the elements, none of which is entirely satisfactory. Nevertheless
most of these attempts agree in large measure in telling us which elements are more electronegative than others. The best-known of
these scales was devised by the Nobel prize-winning California chemist Linus Pauling (1901 to 1994) and is shown in the periodic
table found below. In this scale a value of 4.0 is arbitrarily given to the most electronegative element, fluorine, and the other
electronegativities are scaled relative to this value.

ELECTRONEGATIVITIES OF THE ELEMENTS

→ Atomic radius decreases → Ionization energy increases → Electronegativity increases →
Group (vertical) 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18
Period (horizontal)
1 H He
2.20
2 Li Be B C N O F Ne
0.98 1.57 2.04 2.55 3.04 3.44 3.98
3 Na Mg Al Si P S Cl Ar
0.93 1.31 1.61 1.90 2.19 2.58 3.16
4 K Ca Sc Ti V Cr Mn Fe Co Ni Cu Zn Ga Ge As Se Br Kr
0.82 1.00 1.36 1.54 1.63 1.66 1.55 1.83 1.88 1.91 1.90 1.65 1.81 2.01 2.18 2.55 2.96 3.00
5 Rb Sr Y Zr Nb Mo Tc Ru Rh Pd Ag Cd In Sn Sb Te I Xe
0.82 0.95 1.22 1.33 1.6 2.16 1.9 2.2 2.28 2.20 1.93 1.69 1.78 1.96 2.05 2.1 2.66 2.60
6 Cs Ba * Hf Ta W Re Os Ir Pt Au Hg Tl Pb Bi Po At Rn
0.79 0.89 1.3 1.5 2.36 1.9 2.2 2.20 2.28 2.54 2.00 1.62 2.33 2.02 2.0 2.2 2.2
7 Fr Ra ** Rf Db Sg Bh Hs Mt Ds Rg Cn Uut Uuq Uup Uuh Uus Uuo
0.7 0.9
Lanthanides * La Ce Pr Nd Pm Sm Eu Gd Tb Dy Ho Er Tm Yb Lu
1.1 1.12 1.13 1.14 1.13 1.17 1.2 1.2 1.1 1.22 1.23 1.24 1.25 1.1 1.27
Actinides ** Ac Th Pa U Np Pu Am Cm Bk Cf Es Fm Md No Lr
1.1 1.3 1.5 1.38 1.36 1.28 1.13 1.28 1.3 1.3 1.3 1.3 1.3 1.3 1.3

WHAT IF TWO ATOMS OF EQUAL ELECTRONEGATIVITY BOND TOGETHER?

Consider a bond between two atoms, A and B. If the atoms are equally electronegative, then both atoms have the same tendency to
attract the bonding pair of electrons, and so electrons will be found on average half way between the two atoms.

To get a bond like this, A and B would usually have to be the same element, for example, H2 or Cl2 molecules. Note: It's important to
realize that this is an average picture. The electrons are actually in a molecular orbital, and are moving around all the time within that

2.1.2 Updated 7/7/2019

orbital. This sort of bond could be thought of as being a "pure" or non-polar covalent bond - where the bonding electrons are shared
evenly between the two atoms.

WHAT IF B IS SLIGHTLY MORE ELECTRONEGATIVE THAN A?

If B is slightly more electronegative than A, then B will attract the bonding electron pair more than A.

That means that the B end of the bond will have a greater share of the electron density and so becomes slightly negative. At the same
time, the A end (rather short of electrons) becomes slightly positive. This unequal sharing of the bonding electrons is indicated in the
diagram above using the symbols "δ+" and "δ-". "δ" (read as "delta") means "slightly", so "δ+" means slightly positive, and "δ-"
means slightly negative. Because the electrons are shared unequally, the bond between A and B is polarized, and the bond is
called a polar covalent bond.
A polar covalent bond is a covalent bond in which there is a separation of charge between one end and the other - in other words one
end is slightly positive and the other slightly negative. Examples include most covalent bonds, like the hydrogen-chlorine bond in HCl
or the hydrogen-oxygen bonds in water.

If B is a lot more electronegative than A, then the electron pair is dragged completely over to B's end of the bond. To all intents and
purposes, A has lost control of its electron, and B has complete control over both electrons. Ions have been formed. Because the
electrons are no longer shared, the bond is an ionic bond rather than a covalent bond.

A "SPECTRUM" OF BONDS
There is no clear-cut division between covalent and ionic bonds. In a pure non-polar covalent bond, the electrons are held on average
exactly half way between the atoms. In a polar bond, the electrons have been dragged slightly towards one end. How far does this
dragging have to go before the bond counts as ionic? There is no real answer to that. Sodium chloride is typically considered an ionic
solid, but even here the sodium has not completely lost control of its electron. Because of the properties of sodium chloride, however,
we tend to count it as if it were purely ionic. Lithium iodide, on the other hand, would be described as being "ionic with some covalent
character". In this case, the pair of electrons has not moved entirely over to the iodine end of the bond. Lithium iodide, for example,
dissolves in organic solvents like ethanol - not something which ionic substances normally do. A general rule in organic chemistry is if
the bond is between metal and a non-metal atoms, then the bond should be considered ionic. Examples of this are the lithium - carbon
bond in methyl lithium and the potassium - oxygen bond in potassium tert-butoxide,

Methyl Lithium potassium tert-butoxide

SUMMARY
No electronegativity difference between two atoms leads to a non-polar covalent bond.
A small electronegativity difference leads to a polar covalent bond.
A large electronegativity difference leads to an ionic bond.

EXERCISES
1. Identify the positive and negative ends of each of the bonds shown below.

Answer:

2.1.3 Updated 7/7/2019

1.

QUESTIONS
Q2.1.1
Rank the following from least polar to most polar using knowledge of electronegativity
CH3CH2-Li CH3CH2-K CH3CH2-F CH3CH2-OH
SOLUTIONS
S2.1.1
(least polar) OH < F < Li < K (most polar)
CONTRIBUTORS
Dr. Dietmar Kennepohl FCIC (Professor of Chemistry, Athabasca University)
Prof. Steven Farmer (Sonoma State University)
Organic Chemistry With a Biological Emphasis by Tim Soderberg (University of Minnesota, Morris)
Ed Vitz (Kutztown University), John W. Moore (UW-Madison), Justin Shorb (Hope College), Xavier Prat-Resina (University of
Minnesota Rochester), Tim Wendorff, and Adam Hahn.
Jim Clark (Chemguide.co.uk)

2.1.4 Updated 7/7/2019

2.2: POLAR COVALENT BONDS - DIPOLE MOMENTS
OBJECTIVES
After completing this section, you should be able to
1. explain how dipole moments depend on both molecular shape and bond polarity.
2. predict whether a molecule will possess a dipole moment from the molecular formula or structure.
3. use the presence or absence of a dipole moment as an aid to deducing the structure of a given compound.

KEY TERMS
Make certain that you can define, and use in context, the key term below.
dipole moment

STUDY NOTES
You must be able to combine your knowledge of molecular shapes and bond polarities to determine whether or not a given
compound will have a dipole moment. Conversely, the presence or absence of a dipole moment may also give an important clue to a
compound’s structure. BCl3, for example, has no dipole moment, while NH3 does. This suggests that in BCl3 the chlorines around
boron are in a trigonal planar arrangement, while the hydrogens around nitrogen in NH3 have a less symmetrical arrangement -
trigonal pyramidal.
Remember that the C−H bond is assumed to be non-polar.

MOLECULAR DIPOLE MOMENTS

You previously learned how to calculate the dipole moments of simple diatomic molecules. In more complex molecules with more
than one polar covalent bonds, the three-dimensional geometry and the compound’s symmetry determine whether the molecule has a
net dipole moment.

EXAMPLE 2.2.1 : POLAR BONDS VS. POLAR MOLECULES

In a simple diatomic molecule like H Cl , if the bond is polar, then the whole molecule is polar. What about more complicated
molecules that have more than one bond?

Figure: (left) CCl4 (right) CHCl3

Consider CCl , (left panel in figure above), which as a molecule is not polar - in the sense that it doesn't have an end (or a side)
4

which is slightly negative and one which is slightly positive. The whole of the outside of the molecule is somewhat negative, but
there is no overall separation of charge from top to bottom, or from left to right.
In contrast, CH Cl is a polar molecule (right panel in figure above). The hydrogen at the top of the molecule is less
3

electronegative than carbon and so is slightly positive. This means that the molecule now has a slightly positive "top" and a slightly
negative "bottom", and so is overall a polar molecule.
A polar molecule will need to be "lop-sided" in some way.

Mathematically, dipole moments are vectors; they possess both a magnitude and a direction. The dipole moment of a molecule is
therefore the vector sum of the dipole moments of the individual bonds in the molecule. If the individual bond dipole moments cancel
one another, there is no net dipole moment. Such is the case for CO2, a linear molecule (Figure 2.2.1a). Each C–O bond in CO2 is
polar, yet experiments show that the CO2 molecule has no dipole moment. Because the two C–O bond dipoles in CO2 are equal in
magnitude and oriented at 180° to each other, they cancel. As a result, the CO2 molecule has no net dipole moment even though it has a
substantial separation of charge. In contrast, the H2O molecule is not linear (Figure 2.2.1b); it is bent in three-dimensional space, so
the dipole moments do not cancel each other. Thus a molecule such as H2O has a net dipole moment. We expect the concentration of
negative charge to be on the oxygen, the more electronegative atom, and positive charge on the two hydrogens. This charge
polarization allows H2O to hydrogen-bond to other polarized or charged species, including other water molecules.

2.2.1 Updated 7/7/2019

 Figure 2.2.1 How Individual Bond Dipole Moments Are Added Together to Give an Overall Molecular Dipole Moment for Two
Triatomic Molecules with Different Structures. (a) In CO2, the C–O bond dipoles are equal in magnitude but oriented in opposite
directions (at 180°). Their vector sum is zero, so CO2 therefore has no net dipole. (b) In H2O, the O–H bond dipoles are also equal in
magnitude, but they are oriented at 104.5° to each other. Hence the vector sum is not zero, and H2O has a net dipole moment.
Other examples of molecules with polar bonds are shown in Figure 2.2.2. In molecules like BCl3 and CCl4, that have only one type of
bond and a molecular geometries that are highly symmetrical (trigonal planar and tetrahedral), the individual bond dipole moments
completely cancel, and there is no net dipole moment. However, although a molecule like CHCl3 has a tetrahedral geometry, the atoms
bonded to carbon are not identical. Consequently, the bond dipole moments do not cancel one another, and the result is a molecule
which has a dipole moment.

Figure 2.2.2: Molecules with Polar Bonds. Individual bond dipole moments are indicated in red. Due to their different three-
dimensional structures, some molecules with polar bonds have a net dipole moment (HCl, CH2O, NH3, and CHCl3), indicated in
purple, whereas others do not because the bond dipole moments cancel (BCl3, CCl4, PF5, and SF6).

Molecules with asymmetrical charge distributions have a net dipole moment

EXAMPLE 2.2.1
Which molecule(s) has a net dipole moment?
a. H2S
b. NHF2
c. BF3
Given: three chemical compounds
Asked for: net dipole moment
Strategy:
For each three-dimensional molecular geometry, predict whether the bond dipoles cancel. If they do not, then the molecule has a net
dipole moment.
Solution:
a. The total number of electrons around the central atom, S, is eight, which gives four electron pairs. Two of these electron pairs
are bonding pairs and two are lone pairs, so the molecular geometry of H2S is bent. The bond dipoles cannot cancel one another,
so the molecule has a net dipole moment.

2.2.2 Updated 7/7/2019

 b. Difluoroamine has a trigonal pyramidal molecular geometry. Because there is one hydrogen and two fluorines, and because of
the lone pair of electrons on nitrogen, the molecule is not symmetrical, and the bond dipoles of NHF2 cannot cancel one another.
This means that NHF2 has a net dipole moment. We expect polarization from the two fluorine atoms, the most electronegative
atoms in the periodic table, to have a greater affect on the net dipole moment than polarization from the lone pair of electrons on
nitrogen.

c. The molecular geometry of BF3 is trigonal planar. Because all the B–F bonds are equal and the molecule is highly symmetrical,
the dipoles cancel one another in three-dimensional space. Thus BF3 has a net dipole moment of zero:

EXERCISE 2.2.1
Which molecule(s) has a net dipole moment?
a. CH3Cl
b. SO3
c. XeO3
Answer: CH3Cl; XeO3

EXERCISES
1. Determine whether each of the compounds listed below possesses a dipole moment. For the polar compounds, indicate the direction
of the dipole moment.
a. O=C=O
b. I Cl
c. SO 2

d. CH −O−CH
3 3

e. CH C(=O)CH
3 3

Answers:
1. a.
b.

c.

d.

e.

QUESTIONS
Q2.2.1
The following molecule has no dipole moment in the molecule itself, explain.

Q2.2.2

2.2.3 Updated 7/7/2019

Which of the following molecules has a net dipole?

Q2.2.3
Within reactions with carbonyls, such as a reduction reaction, the carbonyl is attacked from the carbon side and not the oxygen side.
Using knowledge of electronegativity explain why this happens.

SOLUTIONS
S2.2.1
The hydroxyl groups are oriented opposite of one another and therefore the dipole moments
would “cancel” one another out. Therefore having a zero net-dipole.
S2.2.2
1, 3, and 4 have a net dipoles.
S2.2.3
The oxygen is more electronegative than the carbon and therefore creates a dipole along the bond. This leads to having a partial
positive charge on the carbon and the reduction can take place.

CONTRIBUTORS
Dr. Dietmar Kennepohl FCIC (Professor of Chemistry, Athabasca University)
Prof. Steven Farmer (Sonoma State University)
Organic Chemistry With a Biological Emphasis by Tim Soderberg (University of Minnesota, Morris)

2.2.4 Updated 7/7/2019

2.3: FORMAL CHARGES
OBJECTIVES
After completing this section, you should be able to
1. calculate the formal charge of an atom in an organic molecule or ion.
2. identify and recognize the bonding patterns for atoms of carbon, hydrogen, oxygen, nitrogen and the halogens that have a formal
charge of zero.

KEY TERMS
Make certain that you can define, and use in context, the key term below.
valence electrons
bonding and non-bonding electrons
formal charge
carbocations

STUDY NOTES
It is more important that students learn to easily identify atoms that have formal charges of zero, than it is to actually calculate the
formal charge of every atom in an organic compound. Students will benefit by memorizing the "normal" number of bonds and non-
bonding electrons around atoms whose formal charge is equal to zero.

A formal charge compares the number of electrons around a "neutral atom" (an atom not in a molecule) versus the number of
electrons around an atom in a molecule. Formal charge is assigned to an atom in a molecule by assuming that electrons in all chemical
bonds are shared equally between atoms, regardless of relative electronegativity. To calculate formal charges, we assign electrons in the
molecule to individual atoms according to these rules:
Non-bonding electrons are assigned to the atom on which they are located.
Bonding electrons are divided equally between the two bonded atoms, so one electron from each bond goes to each atom.
The formal charge of each atom in a molecule can be calculated using the following equation:

Formal charge = (# of valence e- in neutral atom) - [(# of non-bonding e-) + (# of bonds)] Eqn. 2.3.1

To illustrate this method, let’s calculate the formal charge on the atoms in ammonia (NH3) whose Lewis structure is as follows:

A neutral nitrogen atom has five valence electrons (it is in group 15). From the Lewis structure, the nitrogen atom in ammonia has one
lone pair and three bonds with hydrogen atoms. Substituting into Equation 2.3.1, we obtain

Formal Charge of N = (5 valence e-) - (2 non-bonding e- + 3 bonds) = 0

A neutral hydrogen atom has one valence electron. Each hydrogen atom in the molecule has no non-bonding electrons and one bond.
Using Equation 2.3.1 to calculate the formal charge on hydrogen, we obtain

Formal Charge of H = (1 valence e-) - (0 non-bonding e- + 1 bonds) = 0

The sum of the formal charges of each atom must be equal to the overall charge of the molecule or ion. In this example, the nitrogen
and each hydrogen has a formal charge of zero. When summed the overall charge is zero, which is consistent with the overall neutral
charge of the NH3 molecule.

2.3.1 Updated 7/7/2019

Typically, the structure with the most formal charges of zero on atoms is the more stable Lewis structure. In cases where there MUST
be positive or negative formal charges on various atoms, the most stable structures generally have negative formal charges on the more
electronegative atoms and positive formal charges on the less electronegative atoms. The next example further demonstrates how to
calculate formal charges for polyatomic ions.

EXAMPLE 2.3.1
Calculate the formal charges on each atom in the NH4+ ion.
Given: chemical species
Asked for: formal charges
Strategy:
Identify the number of valence electrons in each atom in the NH4+ ion. Use the Lewis electron structure of NH4+ to identify the
number of bonding and non-bonding electrons associated with each atom and then use Equation 2.3.1 to calculate the formal charge
on each atom.
Solution:
The Lewis electron structure for the NH4+ ion is as follows:

The nitrogen atom in ammonium has zero non-bonding electrons and 4 bonds. Using Equation 2.3.1, the formal charge on the
nitrogen atom is therefore

Formal Charge of N = (5 valence e-) - (0 non-bonding e- + 4 bonds) = +1

Each hydrogen atom in has one bond and zero non-bonding electrons. The formal charge on each hydrogen atom is therefore

Formal Charge of H = (1 valence e-) - (0 non-bonding e- + 1 bonds) = 0

The formal charges on the atoms in the NH4+ ion are thus

Adding together the formal charges on the atoms should give us the total charge on the molecule or ion. In this case, the sum of the
formal charges is 0 + 1 + 0 + 0 + 0 = +1, which is the same a s the overall charge of the ammonium polyatomic ion.

EXERCISE 2.3.1
Write the formal charges on all atoms in BH4−.
Answer:

2.3.2 Updated 7/7/2019

COMMON BONDING PATTERNS IN ORGANIC STRUCTURES
The calculation method reviewed above for determining formal charges on atoms is an essential starting point for a novice organic
chemist, and works well when dealing with small structures. But this method becomes unreasonably time-consuming when dealing
with larger structures. It would be exceptionally tedious to determine the formal charges on each atom in 2'-deoxycytidine (of one of
the four nucleoside building blocks that make up DNA) using equation 2.3.1.

And yet, organic chemists, and especially organic chemists dealing with biological molecules, are expected to draw the structure of
large molecules such as this on a regular basis. Clearly, you need to develop the ability to quickly and efficiently draw large structures
and determine formal charges. Fortunately, this only requires some practice with recognizing common bonding patterns.

CARBON
Carbon, the most important element for organic chemists. In the structures of methane, methanol, ethane, ethene, and ethyne, there are
four bonds to the carbon atom. And each carbon atom has a formal charge of zero. In other words, carbon is tetravalent, meaning that
it commonly forms four bonds.

Carbon is tetravalent in most organic molecules, but there are exceptions. Later in this chapter and throughout this book are examples
of organic ions called ‘carbocations’ and carbanions’, in which a carbon atom has a positive or negative formal charge, respectively.
Carbocations occur when a carbon has only three bonds and no lone pairs of electrons. Carbocations have only 6 valence electrons
and a formal charge of +1. Carbanions occur when the carbon atom has three bonds plus one lone pair of electrons. Carbanions have 8
valence electrons and a formal charge of -1.

Two other possibilities are carbpon radicals and carbenes, both of which have a formal charge of zero. A carbon radical has three
bonds and a single, unpaired electron. Carbon radicals have 7 valence electrons and a formal charge of zero. Carbenes are a highly
reactive species, in which a carbon atom has two bonds and one lone pair of electrons, giving it a formal charge of zero. You may
encounter carbenes in more advanced chemistry courses, but they will not be discussed any further in this book.

2.3.3 Updated 7/7/2019

You should certainly use the methods you have learned to check that these formal charges are correct for the examples given above.
More importantly, you will need, before you progress much further in your study of organic chemistry, to simply recognize these
patterns (and the patterns described below for other atoms) and be able to identify carbons that bear positive and negative formal
charges by a quick inspection.

HYDROGEN
The common bonding pattern for hydrogen is easy: hydrogen atoms in organic molecules typically have only one bond, no unpaired
electrons and a formal charge of zero. The exceptions to this rule are the proton, H+, the hydride ion, H-, and the hydrogen radical, H..
The proton is a hydrogen with no bonds and no lone pairs and a formal charge of +1. The hydride ion is a is a hydrogen with no
bonds, a pair of electrons, and a formal charge of -1. The hydrogen radical is a hydrogen atom with no bonds, a single unpaired
electron and a formal charge of 0. Because this book concentrates on organic chemistry as applied to living things, however, we will
not be seeing ‘naked’ protons and hydrides as such, because they are too reactive to be present in that form in aqueous solution.
Nonetheless, the idea of a proton will be very important when we discuss acid-base chemistry, and the idea of a hydride ion will
become very important much later in the book when we discuss organic oxidation and reduction reactions. As a rule, though, all
hydrogen atoms in organic molecules have one bond, and no formal charge.

OXYGEN
The common arrangement of oxygen that has a formal charge of zero is when the oxygen atom has 2 bonds and 2 lone pairs. Other
arrangements are oxygen with 1 bond and 3 lone pairs, that has a -1 formal charge, and oxygen with 3 bonds and 1 lone pair that has a
formal charge of +1. All three patterns of oxygen fulfill the octet rule.

If it has two bonds and two lone pairs, as in water, it will have a formal charge of zero. If it has one bond and three lone pairs, as in
hydroxide ion, it will have a formal charge of-1. If it has three bonds and one lone pair, as in hydronium ion, it will have a formal
charge of +1.
When we get to our discussion of free radical chemistry in chapter 17, we will see other possibilities, such as where an oxygen atom
has one bond, one lone pair, and one unpaired (free radical) electron, giving it a formal charge of zero. For now, however, concentrate
on the three main non-radical examples, as these will account for virtually everything we see until chapter 17.

NITROGEN
Nitrogen has two major bonding patterns, both of which fulfill the octet rule:

If a nitrogen has three bonds and a lone pair, it has a formal charge of zero. If it has four bonds (and no lone pair), it has a formal
charge of +1. In a fairly uncommon bonding pattern, negatively charged nitrogen has two bonds and two lone pairs.
Two third row elements are commonly found in biological organic molecules: sulfur and phosphorus. Although both of these elements
have other bonding patterns that are relevant in laboratory chemistry, in a biological context sulfur almost always follows the same
bonding/formal charge pattern as oxygen, while phosphorus is present in the form of phosphate ion (PO43-), where it has five bonds

2.3.4 Updated 7/7/2019

(almost always to oxygen), no lone pairs, and a formal charge of zero. Remember that elements in the third row of the periodic table
have d orbitals in their valence shell as well as s and p orbitals, and thus are not bound by the octet rule.

HALOGENS
The halogens (fluorine, chlorine, bromine, and iodine) are very important in laboratory and medicinal organic chemistry, but less
common in naturally occurring organic molecules. Halogens in organic compounds usually are seen with one bond, three lone pairs,
and a formal charge of zero. Sometimes, especially in the case of bromine, we will encounter reactive species in which the halogen has
two bonds (usually in a three-membered ring), two lone pairs, and a formal charge of +1.

These rules, if learned and internalized so that you don’t even need to think about them, will allow you to draw large organic structures,
complete with formal charges, quite quickly.
Once you have gotten the hang of drawing Lewis structures, it is not always necessary to draw lone pairs on heteroatoms, as you can
assume that the proper number of electrons are present around each atom to match the indicated formal charge (or lack thereof).
Occasionally, though, lone pairs are drawn if doing so helps to make an explanation more clear.

USING FORMAL CHARGES TO DISTINGUISH BETWEEN LEWIS STRUCTURES

As an example of how formal charges can be used to determine the most stable Lewis structure for a substance, we can compare two
possible structures for CO2. Both structures conform to the rules for Lewis electron structures.

CO2

1. C is less electronegative than O, so it is the central atom.

2. C has 4 valence electrons and each O has 6 valence electrons, for a total of 16 valence electrons.
3. Placing one electron pair between the C and each O gives O–C–O, with 12 electrons left over.
4. Dividing the remaining electrons between the O atoms gives three lone pairs on each atom:

This structure has an octet of electrons around each O atom but only 4 electrons around the C atom.

5. No electrons are left for the central atom.

6. To give the carbon atom an octet of electrons, we can convert two of the lone pairs on the oxygen atoms to bonding electron pairs.
There are, however, two ways to do this. We can either take one electron pair from each oxygen to form a symmetrical structure or take
both electron pairs from a single oxygen atom to give an asymmetrical structure:

Both Lewis electron structures give all three atoms an octet. How do we decide between these two possibilities? The formal charges for
the two Lewis electron structures of CO2 are as follows:

Both Lewis structures have a net formal charge of zero, but the structure on the right has a +1 charge on the more electronegative atom
(O). Thus the symmetrical Lewis structure on the left is predicted to be more stable, and it is, in fact, the structure observed

2.3.5 Updated 7/7/2019

experimentally. Remember, though, that formal charges do not represent the actual charges on atoms in a molecule or ion. They are
used simply as a bookkeeping method for predicting the most stable Lewis structure for a compound.

NOTE
The Lewis structure with the set of formal charges closest to zero is usually the most stable.

EXAMPLE 2.3.2
The thiocyanate ion (SCN−), which is used in printing and as a corrosion inhibitor against acidic gases, has at least two possible
Lewis electron structures. Draw two possible structures, assign formal charges on all atoms in both, and decide which is the
preferred arrangement of electrons.
Given: chemical species
Asked for: Lewis electron structures, formal charges, and preferred arrangement
Strategy:
A Use the step-by-step procedure to write two plausible Lewis electron structures for SCN−.
B Calculate the formal charge on each atom using Equation 2.3.1.
C Predict which structure is preferred based on the formal charge on each atom and its electronegativity relative to the other atoms
present.
Solution:
A Possible Lewis structures for the SCN− ion are as follows:

B We must calculate the formal charges on each atom to identify the more stable structure. If we begin with carbon, we notice that
the carbon atom in each of these structures shares four bonding pairs, the number of bonds typical for carbon, so it has a formal
charge of zero. Continuing with sulfur, we observe that in (a) the sulfur atom shares one bonding pair and has three lone pairs and
has a total of six valence electrons. The formal charge on the sulfur atom is therefore 6 - (6 + 2/2) = -1. In (b), the sulfur atom has a
formal charge of 0. In (c), the sulfur atom has a formal charge of +1. Continuing with the nitrogen, we observe that in (a) the
nitrogen atom shares three bonding pairs and has one lone pair and has a total of 5 valence electrons. The formal charge on the
nitrogen atom is therefore 5 - (2 + 6/2) = 0. In (b), the nitrogen atom has a formal charge of -1. In (c), the nitrogen atom has a
formal charge of -2.
C Which structure is preferred? Structure (b) is preferred because the negative charge is on the more electronegative atom (N), and
it has lower formal charges on each atom as compared to structure (c): 0, −1 versus +1, −2.

EXERCISE
Salts containing the fulminate ion (CNO−) are used in explosive detonators. Draw three Lewis electron structures for CNO− and use
formal charges to predict which is more stable. (Note: N is the central atom.)
Answer:

The second structure is predicted to be more stable.

EXERCISES
1. Draw the Lewis structure of each of the molecules listed below.
CH3+, NH2−, CH3−, NH4+, BF4−
In each case, use the method of calculating formal charge described to satisfy yourself that the structures you have drawn do in fact
carry the charges shown.
Answer:

2.3.6 Updated 7/7/2019

1.

QUESTIONS
Q2.3.1
Give the formal charges for all non-hydrogen atoms in the following moelcules:
BH4−, H2O, CH3O−
SOLUTIONS
S2.3.1
BH4− (B = −1)
H2O (O = 0)
CH3O− (C = 0, O = −1)

CONTRIBUTORS
Dr. Dietmar Kennepohl FCIC (Professor of Chemistry, Athabasca University)
Prof. Steven Farmer (Sonoma State University)
William Reusch, Professor Emeritus (Michigan State U.), Virtual Textbook of Organic Chemistry
Organic Chemistry With a Biological Emphasis by Tim Soderberg (University of Minnesota, Morris)

2.3.7 Updated 7/7/2019

2.4: RESONANCE
OBJECTIVE
After completing this section, you should be able to
draw resonance forms for molecules and ions.

KEY TERMS
Make certain that you can define, and use in context, the key term below.
resonance form
delocalization

Sometimes, even when formal charges are considered, the bonding in some molecules or ions cannot be described by a single Lewis
structure. Resonance is a way of describing delocalized electrons within certain molecules or polyatomic ions where the bonding
cannot be expressed by a single Lewis formula. A molecule or ion with such delocalized electrons is represented by several
contributing structures (also called resonance structures or canonical forms). Such is the case for ozone (O3), an allotrope of oxygen
with a V-shaped structure and an O–O–O angle of 117.5°.

O3
1. We know that ozone has a V-shaped structure, so one O atom is central:

2. Each O atom has 6 valence electrons, for a total of 18 valence electrons.

3. Assigning one bonding pair of electrons to each oxygen–oxygen bond gives

with 14 electrons left over.

4. If we place three lone pairs of electrons on each terminal oxygen, we obtain

and have 2 electrons left over.

5. At this point, both terminal oxygen atoms have octets of electrons. We therefore place the last 2 electrons on the central atom:

6. The central oxygen has only 6 electrons. We must convert one lone pair on a terminal oxygen atom to a bonding pair of electrons—
but which one? Depending on which one we choose, we obtain either

2.4.1 Updated 7/7/2019

Which is correct? In fact, neither is correct. Both predict one O–O single bond and one O=O double bond. If the bonds were of
different types (one single and one double, for example), they would have different lengths. It turns out, however, that both O–O bond
distances are identical, 127.2 pm, which is shorter than a typical O–O single bond (148 pm) and longer than the O=O double bond in
O2 (120.7 pm).
Equivalent Lewis dot structures, such as those of ozone, are called resonance structures . The position of the atoms is the same in the
various resonance structures of a compound, but the position of the electrons is different. Double-headed arrows link the different
resonance structures of a compound:

Before the development of quantum chemistry it was thought that the double-headed arrow indicates that the actual electronic structure
is an average of those shown, or that the molecule oscillates between the two structures. Today we know that the electrons involved in
the double bonds occupy an orbital that extends over all three oxygen molecules, combining p orbitals on all three (Figure 2.4.1).

Figure 2.4.1: The resonance structure of ozone involves a molecular orbital extending all three oxygen atoms.In ozone, a molecular
orbital extending over all three oxygen atoms is formed from three atom centered pz orbitals. Similar molecular orbitals are found in
every resonance structure.
We will discuss the formation of these molecular orbitals in the next chapter but it is important to understand that resonance structures
are based on molecular orbitals not averages of different bonds between atoms. We describe the electrons in such molecular orbitals as
being delocalized, that is they cannot be assigned to a specific bond between two atoms.

When it is possible to write more than one equivalent resonance structure for a molecule or ion, the actual structure involves a
molecular orbital which is a linear combination of atomic orbitals from each of the atoms.

CO32−
Like ozone, the electronic structure of the carbonate ion cannot be described by a single Lewis electron structure. Unlike O3, though,
the Lewis structures describing CO32− has three equivalent representations.
1. Because carbon is the least electronegative element, we place it in the central position:

2. Carbon has 4 valence electrons, each oxygen has 6 valence electrons, and there are 2 more for the −2 charge. This gives 4 + (3 × 6)
+ 2 = 24 valence electrons.

3. Six electrons are used to form three bonding pairs between the oxygen atoms and the carbon:

4. We divide the remaining 18 electrons equally among the three oxygen atoms by placing three lone pairs on each and indicating the
−2 charge:

2.4.2 Updated 7/7/2019

5. No electrons are left for the central atom.
6. At this point, the carbon atom has only 6 valence electrons, so we must take one lone pair from an oxygen and use it to form a
carbon–oxygen double bond. In this case, however, there are three possible choices:

As with ozone, none of these structures describes the bonding exactly. Each predicts one carbon–oxygen double bond and two carbon–
oxygen single bonds, but experimentally all C–O bond lengths are identical. We can write resonance structures (in this case, three of
them) for the carbonate ion:

As the case for ozone, the actual structure involves the formation of a molecular orbital from pz orbitals centered on each atom and
sitting above and below the plane of the CO32− ion.

EXAMPLE 2.4.1
Benzene is a common organic solvent that was previously used in gasoline; it is no longer used for this purpose, however, because it
is now known to be a carcinogen. The benzene molecule (C6H6) consists of a regular hexagon of carbon atoms, each of which is
also bonded to a hydrogen atom. Use resonance structures to describe the bonding in benzene.
Given: molecular formula and molecular geometry
Asked for: resonance structures
Strategy:
A Draw a structure for benzene illustrating the bonded atoms. Then calculate the number of valence electrons used in this drawing.
B Subtract this number from the total number of valence electrons in benzene and then locate the remaining electrons such that each
atom in the structure reaches an octet.
C Draw the resonance structures for benzene.
Solution:
A Each hydrogen atom contributes 1 valence electron, and each carbon atom contributes 4 valence electrons, for a total of (6 × 1) +
(6 × 4) = 30 valence electrons. If we place a single bonding electron pair between each pair of carbon atoms and between each
carbon and a hydrogen atom, we obtain the following:

Each carbon atom in this structure has only 6 electrons and has a formal charge of +1, but we have used only 24 of the 30 valence
electrons.
B If the 6 remaining electrons are uniformly distributed pair-wise on alternate carbon atoms, we obtain the following:

2.4.3 Updated 7/7/2019

 Three carbon atoms now have an octet configuration and a formal charge of −1, while three carbon atoms have only 6 electrons and
a formal charge of +1. We can convert each lone pair to a bonding electron pair, which gives each atom an octet of electrons and a
formal charge of 0, by making three C=C double bonds.
C There are, however, two ways to do this:

Each structure has alternating double and single bonds, but experimentation shows that each carbon–carbon bond in benzene is
identical, with bond lengths (139.9 pm) intermediate between those typically found for a C–C single bond (154 pm) and a C=C
double bond (134 pm). We can describe the bonding in benzene using the two resonance structures, but the actual electronic
structure is an average of the two. The existence of multiple resonance structures for aromatic hydrocarbons like benzene is often
indicated by drawing either a circle or dashed lines inside the hexagon:

This combination of p orbitals for benzene can be visualized as a ring with a node in the plane of the carbon atoms.

EXERCISE 2.4.1
The sodium salt of nitrite is used to relieve muscle spasms. Draw two resonance structures for the nitrite ion (NO2−).
Answer:

Resonance structures are particularly common in oxyanions of the p-block elements, such as sulfate and phosphate, and in aromatic
hydrocarbons, such as benzene and naphthalene.
EXERCISES
QUESTIONS
Q2.4.1
Draw the resonance structures for the following molecule:

SOLUTIONS
S2.4.1

CONTRIBUTORS

2.4.4 Updated 7/7/2019

Dr. Dietmar Kennepohl FCIC (Professor of Chemistry, Athabasca University)
Prof. Steven Farmer (Sonoma State University)
Organic Chemistry With a Biological Emphasis by Tim Soderberg (University of Minnesota, Morris)

2.4.5 Updated 7/7/2019

2.5: RULES FOR RESONANCE FORMS
OBJECTIVES
After completing this section, you should be able to
determine the relative stability of resonance forms using a set of rules.
use the concept of resonance to explain structural features of molecules and ions.
understand the relationship between resonance and relative stability of molecules and ions.

Rules for estimating stability of resonance structures

1. The resonance form in which all atoms have complete valence shells is more stable.
2. The greater the number of covalent bonds, the greater the stability since more atoms will have complete octets
3. The structure with the least number of formal charges is more stable
4. The structure with the least separation of formal charges is more stable
5. A structure with a negative charge on the more electronegative atom will be more stable
6. Positive charges on the least electronegative atom (most electropositive) is more stable
7. Resonance forms that are equivalent have no difference in stability and contribute equally. (eg. benzene)

The above resonance structures show that the electrons are delocalized within the molecule and through this process the molecule gains
extra stability. Ozone with both of its opposite formal charges creates a neutral molecule and through resonance it is a stable molecule.
The extra electron that created the negative charge one terminal oxygen can be delocalized by resonance through the other terminal
oxygen.
Benzene is an extremely stable molecule due to its geometry and molecular orbital interactions, but most importantly, due to its
resonance structures. The delocalized electrons in the benzene ring make the molecule very stable and with its characteristics of a
nucleophile, it will react with a strong electrophile only and after the first reactivity, the substituted benzene will depend on its
resonance to direct the next position for the reaction to add a second substituent.

EXAMPLE 2.5.1: MULTIPLE RESONANCE OF OTHER MOLECULES

Molecules and ions with more than one resonance form

2.5.1 Updated 7/7/2019

 Some structural resonance conformations are the major contributor or the dominant forms that the molecule exists. For example, if
we look at the above rules for estimating the stability of a molecule, we see that for the third molecule the first and second forms are
the major contributors for the overall stability of the molecule. The nitrogen is more electronegative than carbon so, it can handle
the negative charge more than carbon. A carbon with a negative charge is the least favorable conformation for the molecule to exist,
so the last resonance form contributes very little for the stability of the Ion.

The Hybrid Resonance forms show the different Lewis structures with the electron been delocalized. This is very important for the
reactivity of chloro-benzene because in the presence of an electrophile it will react and the formation of another bond will be
directed and determine by resonance. The lone pair of electrons delocalized in the aromatic substituted ring is where it can
potentially form a new bond with an electrophile, as it is shown there are three possible places that reactivity can take place, the
first to react will take place at the para position with respect to the chloro substituent and then to either ortho position.

EXERCISES
QUESTIONS
Q2.5.1
Are all the bond lengths the same in the following molecule?

SOLUTIONS
S2.5.1

CONTRIBUTORS
Dr. Dietmar Kennepohl FCIC (Professor of Chemistry, Athabasca University)
Prof. Steven Farmer (Sonoma State University)
William Reusch, Professor Emeritus (Michigan State U.), Virtual Textbook of Organic Chemistry

2.5.2 Updated 7/7/2019

Organic Chemistry With a Biological Emphasis by Tim Soderberg (University of Minnesota, Morris)

2.5.3 Updated 7/7/2019

2.6: DRAWING RESONANCE FORMS
OBJECTIVES
After completing this section, you should be able to
draw the resonance structures of molecules or ions that exhibit delocalization.
determine the relative stability of resonance structures using a set of rules.
use the concept of resonance to explain structural features of molecules and ions.

KEY WORDS

resonance structure
resonance hybrid

Resonance is a mental exercise and method within the Valence Bond Theory of bonding that describes the delocalization of electrons
within molecules. It compares and contrasts two or more possible Lewis structures that can represent a particular molecule. Resonance
structures are used when one Lewis structure for a single molecule cannot fully describe the bonding that takes place between
neighboring atoms relative to the empirical data for the actual bond lengths between those atoms. The net sum of valid resonance
structures is defined as a resonance hybrid, which represents the overall delocalization of electrons within the molecule. A molecule
that has several resonance structures is more stable than one with fewer. Some resonance structures are more favorable than others.

INTRODUCTION
Electrons have no fixed position in atoms, compounds and molecules (see image below) but have probabilities of being found in
certain spaces (orbitals). Resonance forms illustrate areas of higher probabilities (electron densities). This is like holding your hat in
either your right hand or your left. The term Resonance is applied when there are two or more possibilities available. Resonance
structures do not change the relative positions of the atoms like your arms in the metaphor. The skeleton of the Lewis Structure remains
the same, only the electron locations change. A double headed arrow on both ends of the arrow ( ↔ ) between Lewis structures is used
to show their inter-connectivity. It is different from the double harpoons ( ⇌ ) used for designating equilibria. A double headed arrow
on only one end ( → ) is used to indicate the movement of two electrons in a single resonance structure.

EXAMPLE 2.6.1: OZONE

Consider ozone (O3)
SOLUTION

Figure: This is an animation of how one can do a resonance with ozone by moving electrons.

DELOCALIZATION AND RESONANCE

STRUCTURES RULES
In resonance structures, the electrons are able to move to help stabilize the molecule. This movement of the electrons is called
delocalization.
1. Resonance structures should have the same number of electrons, do not add or subtract any electrons. (You can check the number of
electrons by counting them)
2. All resonance structures must follow the rules of writing Lewis Structures.
3. The hybridization of the structure must stay the same.

2.6.1 Updated 7/7/2019

4. The skeleton of the structure can not be changed (only the electrons move).
5. Resonance structures must also have the same amount of lone pairs.

FORMAL CHARGE
Even though the structures look the same, the formal charge (FC) may not be. Formal charges are charges that are assigned to a
specific atom in a molecule. If computed correctly, the overall formal charge of the molecule should be the same as the oxidation
charge of the molecule (the charge when you write out the empirical and molecular formula) We want to choose the resonance
structure with the least formal charges that add up to zero or the charge of the overall molecule.
The equation for finding Formal Charge is:
Formal Charge = (number of valence electrons in free orbital) - (number of lone-pair electrons) - ( number bond pair
1

electrons)
The formal charge has to equal the molecule's overall charge.
Ex.) CNS- has an overall charge of -1, so the Lewis structure's formal charge has to equal -1. See Lewis Structure for more information.

EXAMPLE 2.6.2: THIOCYANATE ION

Consider the thiocyanate (CNS-) ion.
SOLUTION
1. Find the Lewis Structure of the molecule. (Remember the Lewis Structure rules.)

2. Resonance: All elements want an octet, and we can do that in multiple ways by moving the terminal atom's electrons around
(bonds too).

3. Assign Formal Charges

Formal Charge = (number of valence electrons in free orbital) - (number of lone-pair electrons) - ( 1

2
number bond pair electrons)
Remember to determine the number of valence electron each atom has before assigning Formal Charges
C = 4 valence e-, N = 5 valence e-, S = 6 valence e-, also add an extra electron for the (-1) charge. The total of valence electrons is
16.

4. Find the most ideal resonance structure. (Note: It is the one with the least formal charges that adds up to zero or to the molecule's
overall charge.)

5. Now we have to look at electronegativity for the "Correct" Lewis structure.

The most electronegative atom usually has the negative formal charge, while the least electronegative atom usually has the positive
formal charges.

2.6.2 Updated 7/7/2019

RESONANCE HYBRIDS
Resonance Structures are a representation of a Resonance Hybrid, which is the combination of all resonance structures. Though the
Formal Charge closest to zero is the most accepted structure, in reality the correct Lewis structure is actually a combination of all the
resonance structures (and hence is not solely describe as one).
1. Draw the Lewis Structure & Resonance for the molecule (using solid lines for bonds).
2. Where there can be a double or triple bond, draw a dotted line (-----) for a bond.
3. Draw only the lone pairs found in all resonance structures, do not include the lone pairs that are not on all of the resonance
structures.

EXAMPLE 2.6.3: CARBONATE ION

Consider the carbonate ion: CO32-
SOLUTION

Step 1: Draw the Lewis Structure & Resonance.

Step 2: Combine the resonance structures by adding (dotted) bonds where other resonance bonds can be formed.

Step 3: Add only the lone pairs found on ALL resonance structures.

2.6.3 Updated 7/7/2019

 The bottom is the finished resonance hybrid for CO32-.

Rules for estimating stability of resonance structures

1. The resonance structure in which all atoms have a complete valence shell is more stable.
2. The greater the number of covalent bonds, the greater the stability since more atoms will have complete octets
3. The structure with the least number of formal charges is more stable
4. The structure with the least separation of formal charge is more stable
5. A structure with a negative charge on the more electronegative atom will be more stable
6. Positive charges on the least electronegative atom (most electropositive) is more stable
7. Resonance forms that are equivalent have no difference in stability and contribute equally. (eg. benzene)

EXAMPLE 2.6.4

The above resonance structures show that the electrons are delocalized within the molecule and through this process the molecule
gains extra stability. Ozone with both of its opposite charges creates a neutral molecule and through resonance it is a stable
molecule. The extra electron that created the negative charge on either terminal oxygen can be delocalized by resonance through the
terminal oxygens.
Benzene is an extremely stable molecule and it is accounted for its geometry and molecular orbital interaction, but most importantly
it's due to its resonance structures. The delocalized electrons in the benzene ring make the molecule very stable and with its
characteristics of a nucleophile, it will react with a strong electrophile only and after the first reactivity, the substituted benzene will
depend on its resonance to direct the next position for the reaction to add a second substituent.
The next molecule, the Amide, is a very stable molecule that is present in most biological systems, mainly in proteins. By studies of
NMR spectroscopy and X-Ray crystallography it is confirmed that the stability of the amide is due to resonance which through
molecular orbital interaction creates almost a double bond between the Nitrogen and the carbon.

EXAMPLE 2.6.5: MULTIPLE RESONANCE OF OTHER MOLECULES

Molecules with more than one resonance form

2.6.4 Updated 7/7/2019

 Some structural resonance conformations are the major contributor or the dominant forms that the molecule exists. For example, if
we look at the above rules for estimating the stability of a molecule, we see that for the third molecule the first and second forms are
the major contributors for the overall stability of the molecule. The nitrogen is more electronegative than carbon so, it can handle
the negative charge more than carbon. A carbon with a negative charge is the least favorable conformation for the molecule to exist,
so the last resonance form contributes very little for the stability of the Ion.

The Hybrid Resonance forms show the different Lewis structures with the electron been delocalized. This is very important for the
reactivity of chloro-benzene because in the presence of an electrophile it will react and the formation of another bond will be
directed and determine by resonance. The lone pair of electrons delocalized in the aromatic substituted ring is where it can
potentially form a new bond with an electrophile, as it is shown there are three possible places that reactivity can take place, the
first to react will take place at the para position with respect to the chloro substituent and then to either ortho position.

REFERENCES
1. Petrucci, Ralph H., et al. General Chemistry: Principles and Modern Applications. New Jersey: Pearson Prentice Hall, 2007. Print.
2. Ahmad, Wan-Yaacob and Zakaria, Mat B. "Drawing Lewis Structures from Lewis Symbols: A Direct Electron Pairing Approach."
Journal of Chemical Education: Journal 77.3: n. pag. Web. March 2000. Link to this journal:
http://pkukmweb.ukm.my/~mbz/c_penerb...83%29/p329.pdf

OUTSIDE LINKS
1. http://en.wikipedia.org/wiki/Resonance_(chemistry)
2. http://www.absoluteastronomy.com/topics/Resonance_(chemistry)#encyclopedia
3. http://www.nku.edu/~russellk/tutorial/reson/resonance.html
4. http://en.wikipedia.org/wiki/Formal_charge
5. http://commons.wikimedia.org/wiki/Main_Page (for the electronegatvity chart)
6. http://misterguch.brinkster.net/PRA037.pdf (for problem 5)
7. http://commons.wikimedia.org/wiki/File:Phosphite-ion-resonance-structures-2D.png (for the (HPO32-) problem 4 answer)
8. http://commons.wikimedia.org/wiki/File:Sulfate-resonance-2D.png (for the Sulfate answer)
9. http://www.mpcfaculty.net/mark_bishop/resonance.htm
10. http://www.chem.ucla.edu/harding/tutorials/resonance/draw_res_str.html

PROBLEMS
1. True or False, The picture below is a resonance structure?

2.6.5 Updated 7/7/2019

2. Draw the Lewis Dot Structure for SO42- and all possible resonance structures. Which of the following resonance structure is not
favored among the Lewis Structures? Explain why. Assign Formal Charges.
3. Draw the Lewis Dot Structure for CH3COO- and all possible resonance structures. Assign Formal Charges. Choose the most
favorable Lewis Structure.
4. Draw the Lewis Dot Structure for HPO32- and all possible resonance structures. Assign Formal Charges.
5. Draw the Lewis Dot Structure for CHO21- and all possible resonance structures. Assign Formal Charges.
6. Draw the Resonance Hybrid Structure for PO43-.
7. Draw the Resonance Hybrid Structure for NO3-.

ANSWERS
1. False, because the electrons were not moved around, only the atoms (this violates the Resonance Structure Rules).
2. Below are the all Lewis dot structure with formal charges (in red) for Sulfate (SO42-). There isn't a most favorable resonance of the
Sulfate ion because they are all identical in charge and there is no change in Electronegativity between the Oxygen atoms.

3. Below is the resonance for CH3COO-, formal charges are displayed in red. The Lewis Structure with the most formal charges is not
desirable, because we want the Lewis Structure with the least formal charge.

4. The resonance for HPO32-, and the formal charges (in red).

2.6.6 Updated 7/7/2019

5. The resonance for CHO21-, and the formal charges (in red).

6. The resonance hybrid for PO43-, hybrid bonds are in red.

7. The resonance hybrid for NO3-, hybrid bonds are in red.

CONTRIBUTORS
Sharon Wei (UCD), Liza Chu (UCD)
Dr. Dietmar Kennepohl FCIC (Professor of Chemistry, Athabasca University)
Prof. Steven Farmer (Sonoma State University)

2.6.7 Updated 7/7/2019

2.7: ACIDS AND BASES - THE BRØNSTED-LOWRY DEFINITION
OBJECTIVES
After completing this section, you should be able to
1. state the Brønsted-Lowry definition of an acid and a base.
2. identify the Brønsted-Lowry acid and base in a given acid-base reaction.
3. identify the conjugate base of an acid and identify the conjugate acid of a base.

KEY TERMS
Make certain that you can define, and use in context, the key terms below.
Brønsted-Lowry acid
Brønsted-Lowry base
conjugate acid
conjugate base

STUDY NOTES
You should already be familiar with the Brønsted-Lowry concept of acidity and the differences between strong and weak acids. You
may wish to review this topic before proceeding.

In 1923, chemists Johannes Brønsted and Martin Lowry independently developed definitions of acids and bases based on compounds
abilities to either donate or accept protons (H+ ions). Here, acids are defined as being able to donate protons in the form of hydrogen
ions; whereas bases are defined as being able to accept protons. This took the Arrhenius definition one step further as water is no
longer required to be present in the solution for acid and base reactions to occur.

BRØNSTED-LOWERY DEFINITION
J.N. Brønsted and T.M. Lowry independently developed the theory of proton donors and proton acceptors in acid-base reactions,
coincidentally in the same region and during the same year. The Arrhenius theory where acids and bases are defined by whether the
molecule produces hydrogen ion or hydroxide ion when dissolved in water was too limiting, because not all chemical reactions,
especially organic reactions, occur in water. The Brønsted-Lowry Theory defines an acid a proton donor, while a base is a proton
acceptor. This is illustrated in the following reactions:
+ −
H Cl + H OH → H3 O + Cl (2.7.1)

+ −
H OH + N H3 → N H + OH (2.7.2)
4

Acid Base
Donates hydrogen ions Accepts hydrogen ions.

HCl HOH → H3O+ + Cl-

HOH NH3→ NH4+ + OH-

The determination of a substance as a Brønsted-Lowry acid or base can only be done by examining the reaction, since many chemicals
can be either an acid or a base. For example, HOH is a base in the first reaction and an acid in the second reaction.

2.7.1 Updated 7/7/2019

To determine whether a substance is an acid or a base, count the hydrogens on each substance before and after the reaction. If the
number of hydrogens has decreased, then that substance is the acid (donates hydrogen ions). If the number of hydrogens has increased,
then that substance is the base (accepts hydrogen ions). These definitions are normally applied to the reactants on the left. If the
reaction is viewed in reverse a new acid and base can be identified. The substances on the right side of the equation are called the
conjugate acid and conjugate base compared to those on the left. Also note that an acid turns into a conjugate base, and the base turns
into the conjugate acid after the reaction is over.

CONJUGATE ACID–BASE PAIRS

In aqueous solutions, acids and bases can be defined in terms of the transfer of a proton from an acid to a base. Thus for every acidic
species in an aqueous solution, there exists a species derived from the acid by the loss of a proton. These two species that differ by only
a proton constitute a conjugate acid–base pair. For example, in the reaction of HCl with water shown below, HCl , the parent acid,
donates a proton to a water molecule, the parent base, thereby forming Cl-. Thus HCl and Cl- constitute a conjugate acid–base pair. By
convention, we always write a conjugate acid–base pair as the acid followed by its conjugate base. In the reverse reaction, the Cl- ion
in solution acts as a base to accept a proton from H3O+, forming H2O and HCl. Thus H3O+ and H2O constitute a second conjugate
acid–base pair. In general, any acid–base reaction must contain two conjugate acid–base pairs, which in this case are HCl/Cl- and
H3O+/H2O.

All acid–base reactions contain two conjugate acid–base pairs.

Similarly, in the reaction of acetic acid with water, acetic acid donates a proton to water, which acts as the base. In the reverse reaction,
H3O+ is the acid that donates a proton to the acetate ion, which acts as the base. Once again, we have two conjugate acid–base pairs:
the parent acid and its conjugate base (CH3CO2H/CH3CO2-) and the parent base and its conjugate acid (H3O+/H2O).

2.7.2 Updated 7/7/2019

In the reaction of ammonia with water to give ammonium ions and hydroxide ions, ammonia acts as a base by accepting a proton from
a water molecule, which in this case means that water is acting as an acid. In the reverse reaction, an ammonium ion acts as an acid by
donating a proton to a hydroxide ion, and the hydroxide ion acts as a base. The conjugate acid–base pairs for this reaction are
NH4+/NH3 and H2O/OH-.

Some common conjugate acid–base pairs are shown in Figure 2.7.1. The strongest acids are at the bottom left, and the strongest bases
are at the top right. The conjugate base of a strong acid is a very weak base, and, conversely, the conjugate acid of a strong base is a
very weak acid.

Figure 2.7.1 The Relative Strengths of Some Common Conjugate Acid–Base Pairs

EXERCISES
1. Identify the Brønsted-Lowry acids and bases in the reactions given below.
a. $\ce{\sf{CH3CH2O^- + H2O <=> CH3CH2OH + OH^- }}$
b. $\ce{\sf{CH3CH2OH + H2SO4 <=> CH3CH2OH2+ + HSO4- }}$
Answer:
1. a.

2.7.3 Updated 7/7/2019

 b.

QUESTIONS
Q2.7.1
Is the following molecule a Brønsted acid or base?
HSO4−
SOLUTIONS
S2.7.1
It can be both, consider the following schemes:

CONTRIBUTORS
Dr. Dietmar Kennepohl FCIC (Professor of Chemistry, Athabasca University)
Organic Chemistry With a Biological Emphasis by Tim Soderberg (University of Minnesota, Morris)
Prof. Steven Farmer (Sonoma State University)

2.7.4 Updated 7/7/2019

2.8: ACID AND BASE STRENGTH
OBJECTIVES
After completing this section, you should be able to
write the expression for the Ka of a weak acid.
convert a given Ka value into a pKa value, and vice versa.
arrange a series of acids in order of increasing or decreasing strength, given their Ka or pKa values.
arrange a series of bases in order of increasing or decreasing strength, given the Ka or pKa values of their conjugate acids.

KEY TERMS
Make certain that you can define, and use in context, the key terms below.
acidity constant, Ka
equilibrium constant, Keq

STUDY NOTES
Calculations and expressions involving Ka and pKa were covered in detail in your first-year general chemistry course. Note that
acidity constant is also known as the acid dissociation constant.

You are no doubt aware that some acids are stronger than others. Sulfuric acid is strong enough to be used as a drain cleaner, as it will
rapidly dissolve clogs of hair and other organic material.

Not surprisingly, concentrated sulfuric acid will also cause painful burns if it touches your skin, and permanent damage if it gets in
your eyes (there’s a good reason for those safety goggles you wear in chemistry lab!). Acetic acid (vinegar), will also burn your skin
and eyes, but is not nearly strong enough to make an effective drain cleaner. Water, which we know can act as a proton donor, is
obviously not a very strong acid. Even hydroxide ion could theoretically act as an acid – it has, after all, a proton to donate – but this is
not a reaction that we would normally consider to be relevant in anything but the most extreme conditions.
The relative acidity of different compounds or functional groups – in other words, their relative capacity to donate a proton to a
common base under identical conditions – is quantified by a number called the acid dissociation constant, abbreviated Ka. The
common base chosen for comparison is water.
We will consider acetic acid as our first example. When a small amount of acetic acid is added to water, a proton-transfer event (acid-
base reaction) occurs to some extent.

Notice the phrase ‘to some extent’ – this reaction does not run to completion, with all of the acetic acid converted to acetate, its
conjugate base. Rather, a dynamic equilibrium is reached, with proton transfer going in both directions (thus the two-way arrows) and
finite concentrations of all four species in play. The nature of this equilibrium situation, as you recall from General Chemistry, is
expressed by an equilibrium constant, K.
The equilibrium constant is actually a ratio of activities (represented by the symbol a), but activities are rarely used in courses other
than analytical or physical chemistry. To simplify the discussion for general chemistry and organic chemistry courses, the activities of
all of the solutes are replaced with molarities, and the activity of the solvent (usually water) is defined as having the value of 1.

2.8.1 Updated 7/7/2019

In our example, we added a small amount of acetic acid to a large amount of water: water is the solvent for this reaction. Therefore, in
the course of the reaction, the concentration of water changes very little, and the water can be treated as a pure solvent, which is always
assigned an activity of 1. The acetic acid, acetate ion and hydronium ion are all solutes, and so their activities are approximated with
molarities. The acid dissociation constant, or Ka, for acetic acid is therefore defined as:
− +
aC H C OO
− ⋅ aH O
+
[CH3 COO ][ H3 O ]
3 3
Keq = ≈ (2.8.1)
aC H C OOH ⋅ aH O [CH3 COOH ][1]
3 2

Because dividing by 1 does not change the value of the constant, the "1" is usually not written, and Ka is written as:
− +
[CH3 COO ][ H3 O ]
−5
Keq = Ka = = 1.75 × 10 (2.8.2)
[CH3 COOH ]

In more general terms, the dissociation constant for a given acid is expressed as:
− +
[A ][ H3 O ]
Ka = (2.8.3)
[H A]

or
+
[A][ H3 O ]
Ka = (2.8.4)
+
[H A ]

Equation 2.8.3 applies to a neutral acid such as like HCl or acetic acid, while Equation 2.8.4 applies to a cationic acid like ammonium
(NH4+).
The value of Ka = 1.75 x 10-5 for acetic acid is very small - this means that very little dissociation actually takes place, and there is
much more acetic acid in solution at equilibrium than there is acetate ion. Acetic acid is a relatively weak acid, at least when compared
to sulfuric acid (Ka = 109) or hydrochloric acid (Ka = 107), both of which undergo essentially complete dissociation in water.
A number like 1.75 x 10- 5 is not very easy either to say or to remember. Chemists often use pKa values as a more convenient term to
express relative acidity. pKa is related to Ka by the following equation

p Ka = − log Ka (2.8.5)

Doing the math, we find that the pKa of acetic acid is 4.8. The use of pKa values allows us to express the acidity of common
compounds and functional groups on a numerical scale of about –10 (very strong acid) to 50 (not acidic at all). Table 2.8.1 at the end
of the text lists exact or approximate pKa values for different types of protons that you are likely to encounter in your study of organic
and biological chemistry. Looking at Table 2.8.1, you see that the pKa of carboxylic acids are in the 4-5 range, the pKa of sulfuric acid
is –10, and the pKa of water is 14. Alkenes and alkanes, which are not acidic at all, have pKa values above 30. The lower the pKa value,
the stronger the acid.
Table 2.8.1: Representative acid constants

2.8.2 Updated 7/7/2019

It is important to realize that pKa is not the same thing as pH: pKa is an inherent property of a compound or functional group, while pH
is the measure of the hydronium ion concentration in a particular aqueous solution:
+
pH = − log[ H3 O ] (2.8.6)

Any particular acid will always have the same pKa (assuming that we are talking about an aqueous solution at room temperature) but
different aqueous solutions of the acid could have different pH values, depending on how much acid is added to how much water.
Our table of pKa values will also allow us to compare the strengths of different bases by comparing the pKavalues of their conjugate
acids. The key idea to remember is this: the stronger the conjugate acid, the weaker the conjugate base. Sulfuric acid is the strongest
acid on our list with a pKa value of –10, so HSO4- is the weakest conjugate base. You can see that hydroxide ion is a stronger base than
ammonia (NH3), because ammonium (NH4+, pKa = 9.2) is a stronger acid than water (pKa = 14.0).

The stronger the conjugate acid, the weaker the conjugate base.

While Table 2.8.1 provides the pKa values of only a limited number of compounds, it can be very useful as a starting point for
estimating the acidity or basicity of just about any organic molecule. Here is where your familiarity with organic functional groups will
come in very handy. What, for example, is the pKaof cyclohexanol? It is not on the table, but as it is an alcohol it is probably
somewhere near that of ethanol (pKa = 16). Likewise, we can use Table 2.8.1 to predict that para-hydroxyphenyl acetaldehyde, an
intermediate compound in the biosynthesis of morphine, has a pKa in the neighborhood of 10, close to that of our reference compound,
phenol.

Notice in this example that we need to evaluate the potential acidity at four different locations on the molecule.

2.8.3 Updated 7/7/2019

Aldehyde and aromatic protons are not at all acidic (pKavalues are above 40 – not on our table). The two protons on the carbon next to
the carbonyl are slightly acidic, with pKa values around 19-20 according to the table. The most acidic proton is on the phenol group, so
if the compound were to be reacted with a single molar equivalent of strong base, this is the proton that would be donated first.
As you continue your study of organic chemistry, it will be a very good idea to commit to memory the approximate pKa ranges of some
important functional groups, including water, alcohols, phenols, ammonium, thiols, phosphates, carboxylic acids and carbons next to
carbonyl groups (so-called a-carbons). These are the groups that you are most likely to see acting as acids or bases in biological organic
reactions.
A word of caution: when using the pKa table, be absolutely sure that you are considering the correct conjugate acid/base pair. If you are
asked to say something about the basicity of ammonia (NH3) compared to that of ethoxide ion (CH3CH2O-), for example, the relevant
pKa values to consider are 9.2 (the pKa of ammonium ion) and 16 (the pKa of ethanol). From these numbers, you know that ethoxide is
the stronger base. Do not make the mistake of using the pKa value of 38: this is the pKa of ammonia acting as an acid, and tells you
how basic the NH2- ion is (very basic!)

EXAMPLE 2.8.1 : ACIDIC GROUPS

Using the pKa table, estimate pKa values for the most acidic group on the compounds below, and draw the structure of the conjugate
base that results when this group donates a proton. Use the pKa table above and/or from the Reference Tables.

Answer:
a. The most acidic group is the protonated amine, pKa ~ 5-9
b. Alpha proton by the C=O group, pKa ~ 18-20
c. Thiol, pKa ~ 10
d. Carboxylic acid, pKa ~ 5
e. Carboxylic acid, pKa ~ 5

EXERCISES
1. Write down an expression for the acidity constant of acetic acid, CH3COOH.

2.8.4 Updated 7/7/2019

2. The pKa of acetic acid is 4.72; calculate its Ka.
3. The Ka of benzoic acid is 6.5 × 10−5; determine its pKa.
4. From your answers to the questions above, determine whether acetic acid or benzoic acid is stronger

ANSWERS
− + − +
[CH3 CO ][ H ] [CH3 CO ][ H3 O ]
2 2
1. Ka = or K
a =
[CH3 CO2 H ] [CH3 CO2 H ]

2. p K a = − log10 Ka = 4.74

−5
Thus, log10 Ka = − 4.72 and K a = anti-log(−4.72)= 1.9 × 10

3. p K a = − log10 Ka = − log10 6.5 × 10

−5
= −(−4.19) = 4.19

4. Benzoic acid is stronger than acetic acid. [Benzoic acid has a higher Ka and a lower pKa.]

CONTRIBUTORS
Dr. Dietmar Kennepohl FCIC (Professor of Chemistry, Athabasca University)
Prof. Steven Farmer (Sonoma State University)
Organic Chemistry With a Biological Emphasis by Tim Soderberg (University of Minnesota, Morris)
Tom Neils (Grand Rapids Community College)

2.8.5 Updated 7/7/2019

2.9: PREDICTING ACID-BASE REACTIONS FROM PKA VALUES
OBJECTIVE
After completing this section, you should be able to
use pKa values to calculate Keq and predict the equilibrium direction of an acid-base reaction.

KEY TERMS
Make certain that you can define, and use in context, the key term below.
pKa

USING PKA VALUES TO PREDICT REACTION EQUILIBRIA

By definition, the pKa value tells us the extent to which an acid will react with water as the base, but by extension, we can also
calculate the equilibrium constant for a reaction between any acid-base pair. Mathematically, it can be shown that:
Keq (for the acid base reaction in question) = 10ΔpKa
where ΔpK is the pK of product acid minus pK of reactant acid
a a a

Consider a reaction between methylamine and acetic acid:

First, we need to identify the acid species on either side of the equation. On the left side, the acid is of course acetic acid, while on the
right side the acid is methyl ammonium. The specific pKa values for these acids are not on our very generalized pKa table, but are
given in the figure above. Without performing any calculations, you should be able to see that this equilibrium lies far to the right-hand
side: acetic acid has a lower pKa, is a stronger acid, and thus it wants to give up its proton more than methyl ammonium does. Doing
the math, we see that
ΔpKa 10.6–4.8 5.8 5
Keq = 10 = 10 = 10 = 6.3 × 10 (2.9.1)

So K is a very large number (much greater than 1) and the equilibrium lies far to the right-hand side of the equation, just as we had
eq

predicted.

If you had just wanted to approximate an answer without bothering to look for a calculator, you could have noted that the difference
in pKa values is approximately 6, so the equilibrium constant should be somewhere in the order of 106, or one million. Using the
pKa table in this way, and making functional group-based pKa approximations for molecules for which we don’t have exact values,
we can easily estimate the extent to which a given acid-base reaction will proceed.

EXAMPLE 2.9.1
Show the products of the following acid-base reactions, and estimate the value of Keq. Use the pKa table from Section 2.8 and/or
from the Reference Tables.

2.9.1 Updated 7/7/2019

 Answer:

EXERCISES
QUESTIONS
Q2.9.1
In the following reactions give the resulting products and label the conjugate acid and bases.

2.9.2 Updated 7/7/2019

SOLUTIONS
S2.9.1

CONTRIBUTORS
Dr. Dietmar Kennepohl FCIC (Professor of Chemistry, Athabasca University)
Prof. Steven Farmer (Sonoma State University)
Organic Chemistry With a Biological Emphasis by Tim Soderberg (University of Minnesota, Morris)

2.9.3 Updated 7/7/2019

2.10: ORGANIC ACIDS AND ORGANIC BASES
OBJECTIVE
After completing this section, you should be able to identify an organic compound as being acidic or basic, given its structure.

This page explains the acidity of simple organic acids and looks at the factors which affect their relative strengths.

ORGANIC ACIDS AS WEAK ACIDS

For the purposes of this topic, we are going to take the definition of an acid as "a substance which donates hydrogen ions (protons) to
other things". We are going to get a measure of this by looking at how easily the acids release hydrogen ions to water molecules when
they are in solution in water.
An acid in solution sets up this equilibrium:
− +
AH(aq) + H2 O(l) ⇌ A + H3 O (2.10.1)
(aq) (aq)

A hydronium ion is formed together with the anion (negative ion) from the acid. This equilibrium is sometimes simplified by leaving
out the water to emphasize the ionization of the acid.
− +
AH(aq) ⇌ A +H (2.10.2)
(aq) (aq)

If you write it like this, you must include the state symbols - "(aq)". Writing H+(aq) implies that the hydrogen ion is attached to a water
molecule as H3O+. Hydrogen ions are always attached to something during chemical reactions.
The organic acids are weak in the sense that this ionization is very incomplete. At any one time, most of the acid will be present in the
solution as un-ionized molecules. For example, in the case of dilute ethanoic acid, the solution contains about 99% of ethanoic acid
molecules - at any instant, only about 1% have actually ionised. The position of equilibrium therefore lies well to the left.

COMPARING THE STRENGTHS OF WEAK ACIDS

The strengths of weak acids are measured on the pKa scale. The smaller the number on this scale, the stronger the acid is. Three of the
compounds we shall be looking at, together with their pKa values are:

Remember - the smaller the number the stronger the acid. Comparing the other two to ethanoic acid, you will see that phenol is very
much weaker with a pKa of 10.00, and ethanol is so weak with a pKa of about 16 that it hardly counts as acidic at all!

NOTE
The smaller the pK , the stronger the acid
a

WHY ARE THESE ACIDS ACIDIC?

In each case, the same bond gets broken - the bond between the hydrogen and oxygen in an -OH group. Writing the rest of the
molecule as "X":

2.10.1 Updated 7/7/2019

If the same bond is being broken in each case, why do these three compounds have such widely different acid strengths?

DIFFERENCES IN ACID STRENGTHS BETWEEN CARBOXYLIC ACIDS, PHENOLS AND ALCOHOLS

Two of the factors which influence the ionization of an acid are:
the strength of the bond being broken,
the stability of the ions being formed.
In these cases, you seem to be breaking the same oxygen-hydrogen bond each time, and so you might expect the strengths to be similar.
The most important factor in determining the relative acid strengths of these molecules is the nature of the ions formed. You always get
a hydroxonium ion - so that's constant - but the nature of the anion (the negative ion) varies markedly from case to case.

EXAMPLE 2.10.1: ETHANOIC ACID (ACETIC ACID)

Ethanoic acid has the structure:

The acidic hydrogen is the one attached to the oxygen. When ethanoic acid ionises it forms the ethanoate ion, CH3COO-.
You might reasonably suppose that the structure of the ethanoate ion was as below, but measurements of bond lengths show that the
two carbon-oxygen bonds are identical and somewhere in length between a single and a double bond.

To understand why this is, you have to look in some detail at the bonding in the ethanoate ion. Like any other double bond, a
carbon-oxygen double bond is made up of two different parts. One electron pair is found on the line between the two nuclei - this is
known as a sigma bond. The other electron pair is found above and below the plane of the molecule in a pi bond. Pi bonds are made
by sideways overlap between p orbitals on the carbon and the oxygen.
In an ethanoate ion, one of the lone pairs on the negative oxygen ends up almost parallel to these p orbitals, and overlaps with them

This leads to a delocalised pi system over the whole of the -COO- group, rather like that in benzene.

All the oxygen lone pairs have been left out of this diagram to avoid confusion. Because the oxygens are more electronegative than
the carbon, the delocalised system is heavily distorted so that the electrons spend much more time in the region of the oxygen
atoms.

2.10.2 Updated 7/7/2019

So where is the negative charge in all this? It has been spread around over the whole of the -COO- group, but with the greatest
chance of finding it in the region of the two oxygen atoms. Ethanoate ions can be drawn simply as:

The dotted line represents the delocalisation. The negative charge is written centrally on that end of the molecule to show that it
isn't localised on one of the oxygen atoms. The more you can spread charge around, the more stable an ion becomes. In this case, if
you delocalise the negative charge over several atoms, it is going to be much less attractive to hydrogen ions - and so you are less
likely to re-form the ethanoic acid.

EXAMPLE 2.10.2: PHENOL

Phenols have an -OH group attached directly to a benzene ring. Phenol itself is the simplest of these with nothing else attached to
the ring apart from the -OH group.

When the hydrogen-oxygen bond in phenol breaks, you get a phenoxide ion, C6H5O-. Delocalization also occurs in this ion. This
time, one of the lone pairs on the oxygen atom overlaps with the delocalised electrons on the benzene ring.

This overlap leads to a delocalisation which extends from the ring out over the oxygen atom. As a result, the negative charge is no
longer entirely localised on the oxygen, but is spread out around the whole ion.

Why then is phenol a much weaker acid than ethanoic acid?

Think about the ethanoate ion again. If there wasn't any delocalization, the charge would all be on one of the oxygen atoms, like
this:

But the delocalisation spreads this charge over the whole of the COO group. Because oxygen is more electronegative than carbon,
you can think of most of the charge being shared between the two oxygens (shown by the heavy red shading in this diagram).

If there wasn't any delocalisation, one of the oxygens would have a full charge which would be very attractive towards hydrogen
ions. With delocalisation, that charge is spread over two oxygen atoms, and neither will be as attractive to a hydrogen ion as if one
of the oxygens carried the whole charge.
That means that the ethanoate ion won't take up a hydrogen ion as easily as it would if there wasn't any delocalisation. Because
some of it stays ionised, the formation of the hydrogen ions means that it is acidic.
In the phenoxide ion, the single oxygen atom is still the most electronegative thing present, and the delocalised system will be
heavily distorted towards it. That still leaves the oxygen atom with most of its negative charge.

2.10.3 Updated 7/7/2019

 What delocalisation there is makes the phenoxide ion more stable than it would otherwise be, and so phenol is acidic to an extent.
However, the delocalisation hasn't shared the charge around very effectively. There is still lots of negative charge around the oxygen
to which hydrogen ions will be attracted - and so the phenol will readily re-form. Phenol is therefore only very weakly acidic.

EXAMPLE 2.10.3: ETHANOL

Ethanol, CH3CH2OH, is so weakly acidic that you would hardly count it as acidic at all. If the hydrogen-oxygen bond breaks to
release a hydrogen ion, an ethoxide ion is formed:

This has nothing at all going for it. There is no way of delocalizing the negative charge, which remains firmly on the oxygen atom.
That intense negative charge will be highly attractive towards hydrogen ions, and so the ethanol will instantly re-form. Since
ethanol is very poor at losing hydrogen ions, it is hardly acidic at all.

VARIATIONS IN ACID STRENGTHS BETWEEN DIFFERENT CARBOXYLIC ACIDS

You might think that all carboxylic acids would have the same strength because each depends on the delocalization of the negative
charge around the -COO- group to make the anion more stable, and so more reluctant to re-combine with a hydrogen ion. In fact, the
carboxylic acids have widely different acidities. One obvious difference is between methanoic acid, HCOOH, and the other simple
carboxylic acids:
pKa
HCOOH 3.75
CH3COOH 4.76
CH3CH2COOH 4.87
CH3CH2CH2COOH 4.82

NOTE
Remember that the higher the value for pKa, the weaker the acid is.

Why is ethanoic acid weaker than methanoic acid? It again depends on the stability of the anions formed - on how much it is possible
to delocalise the negative charge. The less the charge is delocalised, the less stable the ion, and the weaker the acid.
The methanoate ion (from methanoic acid) is:

The only difference between this and the ethanoate ion is the presence of the CH3 group in the ethanoate. But that's important! Alkyl
groups have a tendency to "push" electrons away from themselves. That means that there will be a small amount of extra negative
charge built up on the -COO- group. Any build-up of charge will make the ion less stable, and more attractive to hydrogen ions.
Ethanoic acid is therefore weaker than methanoic acid, because it will re-form more easily from its ions.

The other alkyl groups have "electron-pushing" effects very similar to the methyl group, and so the strengths of propanoic acid and
butanoic acid are very similar to ethanoic acid. The acids can be strengthened by pulling charge away from the -COO- end. You can do
this by attaching electronegative atoms like chlorine to the chain.

As the next table shows, the more chlorines you can attach the better:

2.10.4 Updated 7/7/2019

 pKa
CH3COOH 4.76
CH2ClCOOH 2.86
CHCl2COOH 1.29
CCl3COOH 0.65

Trichloroethanoic acid is quite a strong acid.

Attaching different halogens also makes a difference. Fluorine is the most electronegative and so you would expect it to be most
successful at pulling charge away from the -COO- end and so strengthening the acid.
pKa
CH2FCOOH 2.66
CH2ClCOOH 2.86
CH2BrCOOH 2.90
CH2ICOOH 3.17

The effect is there, but isn't as great as you might expect.

Finally, notice that the effect falls off quite quickly as the attached halogen gets further away from the -COO- end. Here is what
happens if you move a chlorine atom along the chain in butanoic acid.
pKa
CH3CH2CH2COOH 4.82
CH3CH2CHClCOOH 2.84
CH3CHClCH2COOH 4.06
CH2ClCH2CH2COOH 4.52

The chlorine is effective at withdrawing charge when it is next-door to the -COO- group, and much less so as it gets even one carbon
further away.
This page explains why simple organic bases are basic and looks at the factors which affect their relative strengths. For A'level
purposes, all the bases we are concerned with are primary amines - compounds in which one of the hydrogens in an ammonia
molecule, NH3, is replaced either by an alkyl group or a benzene ring.

AMMONIA AS A WEAK BASE

All of the compounds we are concerned with are derived from ammonia and so we'll start by looking at the reason for its basic
properties. For the purposes of this topic, we are going to take the definition of a base as "a substance which combines with hydrogen
ions (protons)". We are going to get a measure of this by looking at how easily the bases take hydrogen ions from water molecules
when they are in solution in water.
Ammonia in solution sets up this equilibrium:
+ −
N H3 + H2 O ⇌ N H + OH (2.10.1)
4

An ammonium ion is formed together with hydroxide ions. Because the ammonia is only a weak base, it doesn't hang on to the extra
hydrogen ion very effectively and so the reaction is reversible. At any one time, about 99% of the ammonia is present as unreacted
molecules. The position of equilibrium lies well to the left.
The ammonia reacts as a base because of the active lone pair on the nitrogen. Nitrogen is more electronegative than hydrogen and so
attracts the bonding electrons in the ammonia molecule towards itself. That means that in addition to the lone pair, there is a build-up
of negative charge around the nitrogen atom. That combination of extra negativity and active lone pair attracts the new hydrogen from
the water.

COMPARING THE STRENGTHS OF WEAK BASES

The strengths of weak bases are measured on the pKb scale. The smaller the number on this scale, the stronger the base is. Three of the
compounds we shall be looking at, together with their pKb values are:

2.10.5 Updated 7/7/2019

Remember - the smaller the number the stronger the base. Comparing the other two to ammonia, you will see that methylamine is a
stronger base, whereas phenylamine is very much weaker.
Methylamine is typical of aliphatic primary amines - where the -NH2 group is attached to a carbon chain. All aliphatic primary
amines are stronger bases than ammonia.
Phenylamine is typical of aromatic primary amines - where the -NH2 group is attached directly to a benzene ring. These are very
much weaker bases than ammonia.

EXPLAINING THE DIFFERENCES IN BASE STRENGTHS

Two of the factors which influence the strength of a base are:
the ease with which the lone pair picks up a hydrogen ion,
the stability of the ions being formed.

WHY ARE ALIPHATIC PRIMARY AMINES STRONGER BASES THAN AMMONIA?

METHYLAMINE
Methylamine has the structure:

The only difference between this and ammonia is the presence of the CH3 group in the methylamine. But that's important! Alkyl
groups have a tendency to "push" electrons away from themselves. That means that there will be a small amount of extra negative
charge built up on the nitrogen atom. That extra negativity around the nitrogen makes the lone pair even more attractive towards
hydrogen ions.

Making the nitrogen more negative helps the lone pair to pick up a hydrogen ion. What about the effect on the positive
methylammonium ion formed? Is this more stable than a simple ammonium ion? Compare the methylammonium ion with an
ammonium ion:

In the methylammonium ion, the positive charge is spread around the ion by the "electron-pushing" effect of the methyl group. The
more you can spread charge around, the more stable an ion becomes. In the ammonium ion there is not any way of spreading the
charge.

2.10.6 Updated 7/7/2019

To summarize:
The nitrogen is more negative in methylamine than in ammonia, and so it picks up a hydrogen ion more readily.
The ion formed from methylamine is more stable than the one formed from ammonia, and so is less likely to shed the hydrogen ion
again.
Taken together, these mean that methylamine is a stronger base than ammonia.

THE OTHER ALIPHATIC PRIMARY AMINES

The other alkyl groups have "electron-pushing" effects very similar to the methyl group, and so the strengths of the other aliphatic
primary amines are very similar to methylamine. For example:
pKb
CH3NH2 3.36
CH3CH2NH2 3.27
CH3CH2CH2NH2 3.16
CH3CH2CH2CH2NH2 3.39

WHY ARE AROMATIC PRIMARY AMINES MUCH WEAKER BASES THAN AMMONIA?
An aromatic primary amine is one in which the -NH2 group is attached directly to a benzene ring. The only one you are likely to come
across is phenylamine. Phenylamine has the structure:

The lone pair on the nitrogen touches the delocalized ring electrons . . .

. . . and becomes delocalized with them:

That means that the lone pair is no longer fully available to combine with hydrogen ions. The nitrogen is still the most electronegative
atom in the molecule, and so the delocalized electrons will be attracted towards it, but the intensity of charge around the nitrogen is
nothing like what it is in, say, an ammonia molecule.
The other problem is that if the lone pair is used to join to a hydrogen ion, it is no longer available to contribute to the delocalisation.
That means that the delocalization would have to be disrupted if the phenylamine acts as a base. Delocalization makes molecules more
stable, and so disrupting the delocalization costs energy and will not happen easily.
Taken together - the lack of intense charge around the nitrogen, and the need to break some delocalization - this means that
phenylamine is a very weak base indeed.

EXERCISES
QUESTIONS
Q2.10.1
Determine which of the one of the molecules is an acid or a base.

2.10.7 Updated 7/7/2019

SOLUTIONS
S2.10.1
1 = Base
2 = Acid
3 = Acid
4 = Acid

CONTRIBUTORS
Jim Clark (Chemguide.co.uk)
Dr. Dietmar Kennepohl FCIC (Professor of Chemistry, Athabasca University)

2.10.8 Updated 7/7/2019

2.11: ACIDS AND BASES - THE LEWIS DEFINITION
OBJECTIVES
After completing this section, you should be able to
1. state the Lewis definition of an acid and a base.
2. identify a given compound as being a Lewis acid or Lewis base, given its Lewis structure or its Kekulé structure.

KEY TERMS
Make certain that you can define, and use in context, the key terms below.
Lewis acid
Lewis base

STUDY NOTES
The Lewis concept of acidity and basicity will be of great use to you when you study reaction mechanisms. The realization that an
ion such as

is electron deficient, and is therefore a Lewis acid, should help you understand why this ion reacts with substances which are Lewis
bases (e.g., H2O).

The Brønsted-Lowry picture of acids and bases as proton donors and acceptors is not the only definition in common use. A broader
definition is provided by the Lewis theory of acids and bases, in which a Lewis acid is an electron-pair acceptor and a Lewis base is an
electron-pair donor. This definition covers Brønsted-Lowry proton transfer reactions, but also includes reactions in which no proton
transfer is involved. The interaction between a magnesium cation (Mg+2) and a carbonyl oxygen is a common example of a Lewis
acid-base reaction. The carbonyl oxygen (the Lewis base) donates a pair of electrons to the magnesium cation (the Lewis acid).

As we will see in Chapter 19 when we begin the study of reactions involving carbonyl groups, this interaction has the very important
effect of increasing the polarity of the carbon-oxygen double bond. The Brønsted-Lowry equivalent of the reaction above is simply
protonation of the carbonyl group. This, too, has the effect of increasing the polarity of the carbonyl double bond.

While it is important to be familiar with the Lewis definition, the focus throughout the remainder of this chapter will be on acid-base
reactions of the Brønsted-Lowry type, where an actual proton transfer event takes place.

LEWIS ACIDS
Borane is unusual because it is a compound without an octet. The central boron atom has only six valence electrons. It needs one more
pair of electrons to obtain an octet. The boron is a Lewis acid.

2.11.1 Updated 7/7/2019

 Figure 2.11.1: Borane is a Lewis acid. It can accept electrons from a donor atom. The square drawn beside the boron is used to
reinforce the idea that there is a vacant site for electrons there.
Lewis acids are often short of a complete octet.
In the main group of the periodic table, atoms in the Group 13 column (including boron and aluminum) have three valence electrons to
share in order to make bonds. Sharing these electrons with three electrons from neighbors would make three bonds, and provide six
electrons, not eight, in the valence shell. Another pair of electrons must be accepted from a donor to achieve an octet.

Figure 2.11.2: Boron, aluminum and indium are from the same column of the periodic table. All three are often Lewis acidic; they can
accept electrons from donors.
Boron, aluminum and indium compounds are often Lewis acids.
The eight-electron rule does not hold throughout the periodic table. In order to obtain noble gas configurations, some atoms may need
eighteen electrons in their valence shell. For example, transition metals such as titanium often follow an eighteen-electron rule.
Titanium has four valence electrons and can form four bonds in compounds such as titanium tetrakis (isopropoxide), below, or titanium
tetrachloride, TiCl4. However, the titanium atom in that compound has only eight valence electrons, not eighteen. It can easily accept
electrons from donors.

Figure 2.11.3: Although titanium has eight electrons in this molecule, titanium tetrakis(isopropoxide), it can accommodate up to
eighteen. It is Lewis acidic. The cerium atom in cerium tris(dimethylamide) comes from a similar part of the periodic table and is also
Lewis acidic.
Transition metals such as titanium, iron and nickel may have up to eighteen electrons and can frequently accept electron pairs from
Lewis bases. Transition metals are often Lewis acids.
Lanthanides such as cerium and samarium could conceivably have up to thirty-two electrons in their valence shells! They never do.
However, they are usually strong Lewis acids.
Positive ions are often Lewis acids because they have an electrostatic attraction for electron donors. Examples include alkali and
alkaline earth metals in the group IA and IIA columns. K+, Mg2+ and Ca2+ are sometimes seen as Lewis acidic sites in biology, for
example. These ions are very stable forms of these elements because of their low electron ionization potentials. However, their positive
charges do attract electron donors.

2.11.2 Updated 7/7/2019

 Figure 2.11.4. A calcium ion essentially has a noble gas configuration. Nevertheless, its positive charge can attract electrons from a
donor atom.
In a similar way, "early" transition metals -- those that are close to the left hand side of the periodic table, especially in groups IIIB,
IVB and VB -- have low ionization potentials and have high positive charges or oxidation states. For example, Sc3+, Zr4+ and V5+ are
common forms of some early transition metals, and they are strong Lewis acids.

Figure 2.11.5: A few alkali, alkaline earth and transition metals that are commonly found as cations.
Many cations such as Ca2+ or Sc3+ are good Lewis acids. Their positive charges attract electrons.

THE PROTON AS A COMMON LEWIS ACID

Perhaps the most common example of a Lewis acid or electrophile is also the simplest. It is the hydrogen cation or proton. It is called a
proton because, in most hydrogen atoms, the only particle in the nucleus is a proton. If an electron is removed to make a cation, a
proton is all that is left.
H+ is a very common Lewis acid or electrophile.
A proton is electrophilic for a couple of reasons. It has a positive charge, and so it will attract electrons, which are negative. Also, it
lacks the electron configuration of its noble gas neighbor, helium. Helium has two electrons. If a Lewis base or nucleophile donates a
pair of electrons to a proton, the proton will obtain a Noble gas configuration. That's part of the reason why, in some periodic tables,
hydrogen is shown in two places: at the very left, illustrating its potential to lose an electron, like sodium and lithium; and at the right,
illustrating its potential to take on helium's configuration.

Figure 2.11.6: Proton as Lewis acid.

There is something about hydrogen cations that is not so simple, however. They are actually not so common. Instead, protons are
generally always bound to a Lewis base. Hydrogen is almost always covalently (or datively / coordinately) bonded to another atom.
Many of the other elements commonly found in compounds with hydrogen are more electronegative than hydrogen. As a result,
hydrogen often has a partial positive charge. Remember, that is one of the reasons that atoms can act as Lewis acids: with a partial
positive charge, an atom becomes electrophilic.
Our statement about protons might better be expressed as:
H+ is a very common Lewis acid or electrophile.

Figure 2.11.7. Proton transfer from one site to another.

If hydrogens are almost always bonded to other atoms, then the Lewis acid-base interactions we have looked at so far are slightly
different here. Instead of two compounds coming together and forming a bond, we have one Lewis base replacing another at a proton.
Protons are transferred from one basic site to another.
Transfer occurs by donation of a lone pair to the proton.

LEWIS BASES
What makes a molecule (or an atom or ion) a Lewis base? It must have a pair of electrons available to share with another atom to form
a bond. The most readily available electrons are those that are not already in bonds. Bonding electrons are low in energy. Non-bonding
electrons are higher in energy and may be stabilized when they are delocalized in a new bond.
Lewis bases usually have non-bonding electrons or lone pairs.

2.11.3 Updated 7/7/2019

 NOTE 1: AMMONIA
Ammonia, NH3, has a lone pair and is a Lewis base. It can donate to compounds that will accept electrons.

Ammonia donating to an electron acceptor or Lewis acid.

Lewis bases may be anionic or neutral. The basic requirement is that they have a pair of electrons to donate. Examples of Lewis bases
include halide ions such as bromide or chloride. To the right of the halides in the periodic table are Noble gases such as neon. Noble
gases do have lone pairs, but are stable enough that they do not usually react. They are not very good Lewis bases. To the left of the
halides, however, are other examples in oxygen and nitrogen compounds. Water also has lone pairs and is a common Lewis base, and
so is hydroxide ion, HO-.

Figure 2.11.2: Some examples of Lewis basic ions and molecules. Note that neon, although it has nonbonding electron pairs or lone
pairs, does not usually act as a Lewis base.
Halides, water, ammonia and hydroxide ion are examples of Lewis bases.
One column further to the left in the periodic table from nitrogen is carbon. Carbon does not normally have a lone pair. For example,
methane, CH4, has all of its valence electrons in bonding pairs. These bonding pairs are too stable to donate under normal conditions.
Methane is not a Lewis base.

Figure 2.11.3. Carbon and boron "hydrides". Neither of these compounds has a lone pair, and neither is a good Lewis base.

Even further to the left is boron. A simple boron compound is borane, BH3. Borane has no lone pairs; all its valence electrons are in
bonds. Boron is not a good Lewis base.
PROBLEM
Which of the following compounds appear to be Lewis bases?
a) SiH4 b) AlH3 c) PH3 d) SH2 e) -SH
LEWIS ACID-BASE COMPLEXES
What happens when a Lewis base donates a pair of electrons to a Lewis acid? The arrow formulism we have been using to illustrate the
behaviour of Lewis acids and Lewis bases is meant to show the direction of electron movement from the donor to the acceptor.
However, given that a bond can be thought of as a pair of electrons that are shared between two atoms (in this case, between the donor
and the acceptor), these arrows also show where bonds are forming.

Figure AB4.1. Donation of electrons from a Lewis base to a Lewis acid.

2.11.4 Updated 7/7/2019

The electrons donated from a Lewis base to a Lewis acid form a new bond. A new, larger compound is formed from the smaller Lewis
acid and Lewis base. This compound is called a Lewis acid-base complex.
A simple example of Lewis acid-base complexation involves ammonia and boron trifluoride. The nitrogen atom has a lone pair and is
an electron donor. The boron has no octet and is an electron acceptor. The two compounds can form a Lewis acid-base complex or a
coordination complex together.

Figure AB4.2: Formation of a Lewis acid-base complex from ammonia and boron trifluoride.
When the nitrogen donates a pair of electrons to share with the boron, the bond that forms is sometimes called a coordinate bond.
Another term for this kind of bond is a dative bond. A coordinate or dative bond is any covalent bond that arose because one atom
brought a pair of its electrons and donated them with another.
There is another piece of terminology you should get used to here. Sometimes, the electron donor is called a nucleophile and the
electron acceptor is called an electrophile. Ammonia is a nucleophile and boron trifluoride is an electrophile.
Because Lewis bases are attracted to electron-deficient atoms, and because positive charge is generally associated with the nucleus
of an atom, Lewis bases are sometimes refered to as "nucleophiles". Nucleophile means nucleus-loving.
Because Lewis acids attract electron pairs, Lewis acids are sometimes called "electrophiles". Electrophile meanse electron-loving.
Lewis acid-base complexes frequently have very different properties from the separate compounds from which they were formed. For
example, titanium tetrachloride is a yellow liquid at room temperature. It is so Lewis acidic that it reacts with moisture in the air,
undergoing a reaction that generates HCl gas in the form of white smoke. Tetrahydrofuran (or THF), a mild Lewis base, is a colourless
liquid. When THF and TiCl4 are combined, a Lewis acid-base complex is formed, TiCl4(THF)2. TiCl4(THF)2 is a yellow solid at room
temperature. Although it still reacts with the air, it does so very slowly, and shows no visible change when exposed to the air for
several minutes.

Figure AB4.5: A Lewis acid-base complex between tetrahydrofuran (THF) and titanium tetrachloride.
PROBLEM 1
Show, using arrow notation, the reaction between THF and titanium tetrachloride to form the Lewis acid-base complex, TiCl4(THF)2.
Also show the structures of the complexes formed.
PROBLEM 2
A similar Lewis acid-base complex is formed between THF and borane, BH3.
1. Which compound is the Lewis acid? Which one is the Lewis base?
2. Which atom in the Lewis acid is the acidic site? Why?
3. Which atom in the Lewis base is the basic site? Why?
4. How many donors would be needed to satisfy the acidic site?
5. Show, using arrow notation, the reaction to form a Lewis acid-base complex.
6. Borane is highly pyrophoric; it reacts violently with air, bursting into flames. Show, using arrow notation, what might be happening
when borane contacts the air.
7. Borane-THF complex is much less pyrophoric than borane. Why do you suppose that is so?
PROBLEM 3
When a neutral Lewis acid combines with an anionic Lewis base, the product is called a complex ion. The same is true if a cationic
Lewis acid combines with a neutral Lewis base.
Show the formation of the following polyatomic anions from the Lewis acid-base pairs that were combined in each case.
a) BF4- b) PF6- c) AlCl4- d) AlH4- e) Ag(NH3)2+

EXERCISES
QUESTIONS

2.11.5 Updated 7/7/2019

Q2.11.1
For the following molecules state wither they are Lewis acid or base and wither or not they are a Brønsted acid or base.

SOLUTIONS
S2.11.1
Acetone is a Lewis base and a Brønsted base. Ammonium cation is both a Lewis acid and a weak Brønsted acid.

CONTRIBUTORS
Dr. Dietmar Kennepohl FCIC (Professor of Chemistry, Athabasca University)
Prof. Steven Farmer (Sonoma State University)
Chris P Schaller, Ph.D., (College of Saint Benedict / Saint John's University)
Organic Chemistry With a Biological Emphasis by Tim Soderberg (University of Minnesota, Morris)

2.11.6 Updated 7/7/2019

2.12: MOLECULAR MODELS
OBJECTIVE
After completing this section, you should be able to use ball-and-stick molecular models to make models of simple organic
compounds (e.g., ethane, ethylene, acetylene, ethanol, formaldehyde, acetone, acetic acid), given their Kekulé structures or
molecular formulas.

STUDY NOTES
You will have noticed that we have given two names for most of the compounds discussed up to this point. In general we shall be
using systematic (i.e., IUPAC—International Union of Pure and Applied Chemistry) names throughout the course. However, simple
compounds are often known principally by their common names, which may be more familiar to you than their IUPAC
counterparts. We shall address the subject of nomenclature (naming) in Chapter 3.
ethanol,

formaldehyde (methanal),

acetone (propanone),

acetic (ethanoic) acid,

EXERCISES
1. Construct a molecular model of each of the compounds listed below.
a. CH 3
−CN

b. CH 3
−N=C=O

c. CH 3
−CH −O−CH
2 3

Hint: Use the curved sticks to form the multiple bonds and the straight sticks for single bonds.

ANSWERS:
A.

B.

C.

CONTRIBUTORS
Dr. Dietmar Kennepohl FCIC (Professor of Chemistry, Athabasca University)

2.12.1 Updated 7/7/2019

2.13: POLAR COVALENT BONDS; ACIDS AND BASES (SUMMARY)

2.13.1 Updated 7/7/2019

3: ORGANIC COMPOUNDS: ALKANES AND THEIR STEREOCHEMISTRY
This chapter begins with an introduction to the concept of the functional group, a concept that facilitates the systematic study of organic
chemistry. Next, we introduce the fundamentals of organic nomenclature (i.e., the naming of organic chemicals) through examination of
the alkane family of compounds. We then discuss, briefly, the occurrence and properties of alkanes, and end with a description of cis-
trans isomerism in cycloalkanes.

3.1: CHAPTER OBJECTIVES

3.2: FUNCTIONAL GROUPS
Functional groups are atoms or small groups of atoms (two to four) that exhibit a characteristic reactivity. A particular functional group
will almost always display its characteristic chemical behavior when it is present in a compound. Because of their importance in
understanding organic chemistry, functional groups have characteristic names that often carry over in the naming of individual
compounds incorporating specific groups

3.3: ALKANES AND ALKANE ISOMERS

Alkanes are organic compounds that consist entirely of single-bonded carbon and hydrogen atoms and lack any other functional groups.
Alkanes have the general formula CnH2n+2 and can be subdivided into the following three groups: the linear straight-chain alkanes,
branched alkanes, and cycloalkanes. Alkanes are also saturated hydrocarbons. Cycloalkanes are cyclic hydrocarbons, meaning that the
carbons of the molecule are arranged in the form of a ring.

3.4: ALKYL GROUPS

The IUPAC system requires first that we have names for simple unbranched chains, as noted above, and second that we have names for
simple alkyl groups that may be attached to the chains. Examples of some common alkyl groups are given in the following table. Note
that the "ane" suffix is replaced by "yl" in naming groups. The symbol R is used to designate a generic (unspecified) alkyl group.

3.5: NAMING ALKANES

3.6: PROPERTIES OF ALKANES
Alkanes are not very reactive and have little biological activity; all alkanes are colorless and odorless.

3.7: CONFORMATIONS OF ETHANE

Conformational isomerism involves rotation about sigma bonds, and does not involve any differences in the connectivity or geometry of
bonding. Two or more structures that are categorized as conformational isomers, or conformers, are really just two of the exact same
molecule that differ only in terms of the angle about one or more sigma bonds.

3.8: CONFORMATIONS OF OTHER ALKANES

3.9: GASOLINE - A DEEPER LOOK
The petroleum that is pumped out of the ground at locations around the world is a complex mixture of several thousand organic
compounds, including straight-chain alkanes, cycloalkanes, alkenes, and aromatic hydrocarbons with four to several hundred carbon
atoms. The identities and relative abundances of the components vary depending on the source.

TOC.1 Updated 7/14/2019

3.1: CHAPTER OBJECTIVES
After you have completed Chapter 3, you should be able to
1. fulfill the detailed objectives listed under each section.
2. identify some of the commonest functional groups.
3. write the structures and names of the first ten straight-chain alkanes.
4. recognize and name the simple alkyl substituents, and give the systematic names for branched-chain alkanes.
5. briefly describe some of the processes used during the refining of petroleum.
6. briefly describe the physical properties of alkanes.
7. draw a number of possible conformations of some simple alkanes and alkane-like compounds, and represent the energies of such
conformations on energy versus rotation diagrams.
8. define, and use in context, the key terms introduced in this chapter.

CONTRIBUTORS
Dr. Dietmar Kennepohl FCIC (Professor of Chemistry, Athabasca University)

3.1.1 Updated 7/7/2019

3.2: FUNCTIONAL GROUPS
OBJECTIVES
After completing this section, you should be able to
1. explain why the properties of a given organic compound are largely dependent on the functional group or groups present in the
compound.
2. identify the functional groups present in each of the following compound types: alkenes, alkynes, arenes, (alkyl and aryl)
halides, alcohols, ethers, aldehydes, ketones, esters, carboxylic acids, (carboxylic) acid chlorides, amides, amines, nitriles, nitro
compounds, sulfides and sulfoxides.
3. identify the functional groups present in an organic compound, given its structure.
4. Given the structure of an organic compound containing a single functional group, identify which of the compound types listed
under Objective 2, above, it belongs to.
5. draw the structure of a simple example of each of the compound types listed in Objective 2.

KEY TERMS
Make certain that you can define, and use in context, the key term below.
functional group

STUDY NOTES
The concept of functional groups is a very important one. We expect that you will need to refer back to tables at the end of Section
3.1 quite frequently at first, as it is not really feasible to learn the names and structures of all the functional groups and compound
types at one sitting. Gradually they will become familiar, and eventually you will recognize them automatically.

Functional groups are atoms or small groups of atoms (two to four) that exhibit a characteristic reactivity. A particular functional
group will almost always display its characteristic chemical behavior when it is present in a compound. Because of their importance in
understanding organic chemistry, functional groups have characteristic names that often carry over in the naming of individual
compounds incorporating specific groups
As we progress in our study of organic chemistry, it will become extremely important to be able to quickly recognize the most common
functional groups, because they are the key structural elements that define how organic molecules react. For now, we will only worry
about drawing and recognizing each functional group, as depicted by Lewis and line structures. Much of the remainder of your study of
organic chemistry will be taken up with learning about how the different functional groups tend to behave in organic reactions.

HYDROCARBONS AND HALIDES

We have already seen some examples of very common functional groups: ethene, for example, contains a carbon-carbon double bond.
This double bond is referred to, in the functional group terminology, as an alkene.

The carbon-carbon triple bond in ethyne is the simplest example of an alkyne function group.
What about ethane? All we see in this molecule is carbon-hydrogen and carbon-carbon single bonds, so in a sense we can think of
ethane as lacking a functional group entirely. However, we do have a general name for this ‘default’ carbon bonding pattern: molecules
or parts of molecules containing only carbon-hydrogen and carbon-carbon single bonds are referred to as alkanes. If the carbon of an
alkane is bonded to a halogen, the group is now referred to as a haloalkane (fluoroalkane, chloroalkane, etc.). Chloroform, CHCl3, is
an example of a simple haloalkane.
ALCOHOLS AND THIOLS
We have already seen the simplest possible example of an alcohol functional group in methanol. In the alcohol functional group, a
carbon is single-bonded to an OH group (this OH group, by itself, is referred to as a hydroxyl). If the central carbon in an alcohol is
bonded to only one other carbon, we call the group a primary alcohol. In secondary alcohols and tertiary alcohols, the central carbon is
bonded to two and three carbons, respectively. Methanol, of course, is in class by itself in this respect.

3.2.1 Updated 7/7/2019

The sulfur analog of an alcohol is called a thiol (the prefix thio, derived from the Greek, refers to sulfur).

In an ether functional group, a central oxygen is bonded to two carbons. Below are the line and Lewis structures of diethyl ether, a
common laboratory solvent and also one of the first medical anaesthesia agents.

In sulfides, the oxygen atom of an ether has been replaced by a sulfur atom.

AMINES AND PHOSPHATES

Ammonia is the simplest example of a functional group called amines. Just as there are primary, secondary, and tertiary alcohols, there
are primary, secondary, and tertiary amines.

One of the most important properties of amines is that they are basic, and are readily protonated to form ammonium cations.

Phosphorus is a very important element in biological organic chemistry, and is found as the central atom in the phosphate group. Many
biological organic molecules contain phosphate, diphosphate, and triphosphate groups, which are linked to a carbon atom by the
phosphate ester functionality.

Because phosphates are so abundant in biological organic chemistry, it is convenient to depict them with the abbreviation 'P'. Notice
that this 'P' abbreviation includes the oxygen atoms and negative charges associated with the phosphate groups.

3.2.2 Updated 7/7/2019

CARBONYL CONTAINING FUNCTIONAL GROUPS
ALDEHYDES AND KETONES
There are a number of functional groups that contain a carbon-oxygen double bond, which is commonly referred to as a carbonyl.
Ketones and aldehydes are two closely related carbonyl-based functional groups that react in very similar ways. In a ketone, the
carbon atom of a carbonyl is bonded to two other carbons. In an aldehyde, the carbonyl carbon is bonded on one side to a hydrogen,
and on the other side to a carbon. The exception to this definition is formaldehyde, in which the carbonyl carbon has bonds to two
hydrogens.

Molecules with carbon-nitrogen double bonds are called imines, or Schiff bases.

CARBOXYLIC ACIDS AND ACID DERIVATIVES

If a carbonyl carbon is bonded on one side to a carbon (or hydrogen) and on the other side to a heteroatom (in organic chemistry, this
term generally refers to oxygen, nitrogen, sulfur, or one of the halogens), the functional group is considered to be one of the
‘carboxylic acid derivatives’, a designation that describes a grouping of several functional groups. The eponymous member of this
grouping is the carboxylic acid functional group, in which the carbonyl is bonded to a hydroxyl (OH) group.

As the name implies, carboxylic acids are acidic, meaning that they are readily deprotonated to form the conjugate base form, called a
carboxylate (much more about carboxylic acids in the acid-base chapter!).

In amides, the carbonyl carbon is bonded to a nitrogen. The nitrogen in an amide can be bonded either to hydrogens, to carbons, or to
both. Another way of thinking of an amide is that it is a carbonyl bonded to an amine.

In esters, the carbonyl carbon is bonded to an oxygen which is itself bonded to another carbon. Another way of thinking of an ester is
that it is a carbonyl bonded to an alcohol. Thioesters are similar to esters, except a sulfur is in place of the oxygen.

3.2.3 Updated 7/7/2019

In an acyl phosphate, the carbonyl carbon is bonded to the oxygen of a phosphate, and in an acid chloride, the carbonyl carbon is
bonded to a chlorine.

Finally, in a nitrile group, a carbon is triple-bonded to a nitrogen. Nitriles are also often referred to as cyano groups.

A single compound often contains several functional groups. The six-carbon sugar molecules glucose and fructose, for example,
contain aldehyde and ketone groups, respectively, and both contain five alcohol groups (a compound with several alcohol groups is
often referred to as a ‘polyol’).

Capsaicin, the compound responsible for the heat in hot peppers, contains phenol, ether, amide, and alkene functional groups.

The male sex hormone testosterone contains ketone, alkene, and secondary alcohol groups, while acetylsalicylic acid (aspirin) contains
aromatic, carboxylic acid, and ester groups.

While not in any way a complete list, this section has covered most of the important functional groups that we will encounter in
biological and laboratory organic chemistry. The table on the inside back cover provides a summary of all of the groups listed in this
section, plus a few more that will be introduced later in the text.

PROBLEMS
1: Identify the functional groups in the following organic compounds. State whether alcohols and amines are primary, secondary, or
tertiary.

3.2.4 Updated 7/7/2019

2: Draw one example each (there are many possible correct answers) of compounds fitting the descriptions below, using line structures.
Be sure to designate the location of all non-zero formal charges. All atoms should have complete octets (phosphorus may exceed the
octet rule).
a) a compound with molecular formula C6H11NO that includes alkene, secondary amine, and primary alcohol functional groups
b) an ion with molecular formula C3H5O6P 2- that includes aldehyde, secondary alcohol, and phosphate functional groups.
c) A compound with molecular formula C6H9NO that has an amide functional group, and does not have an alkene group.
SOLUTION
1:
a) carboxylate, sulfide, aromatic, two amide groups (one of which is cyclic)
b) tertiary alcohol, thioester
c) carboxylate, ketone
d) ether, primary amine, alkene

FUNCTIONAL GROUP TABLES

EXCLUSIVELY CARBON FUNCTIONAL GROUPS
Group Formula Class Name Specific Example IUPAC Name Common Name

Alkene H2C=CH2 Ethene Ethylene

Alkyne HC≡CH Ethyne Acetylene

Arene C6H6 Benzene Benzene

FUNCTIONAL GROUPS WITH SINGLE BONDS TO HETEROATOMS

3.2.5 Updated 7/7/2019

 Group Formula Class Name Specific Example IUPAC Name Common Name
Halide H3C-I Iodomethane Methyl iodide

Alcohol CH3CH2OH Ethanol Ethyl alcohol

Ether CH3CH2OCH2CH3 Diethyl ether Ether

Amine H3C-NH2 Aminomethane Methylamine

Nitro Compound H3C-NO2 Nitromethane

Thiol H3C-SH Methanethiol Methyl mercaptan

Sulfide H3C-S-CH3 Dimethyl sulfid

FUNCTIONAL GROUPS WITH MULTIPLE BONDS TO HETEROATOMS

3.2.6 Updated 7/7/2019

 Group Formula Class Name Specific Example IUPAC Name Common Name

Nitrile H3C-CN Ethanenitrile Acetonitrile

Aldehyde H3CCHO Ethanal Acetaldehyde

Ketone H3CCOCH3 Propanone Acetone

Carboxylic Acid H3CCO2H Ethanoic Acid Acetic acid

Ester H3CCO2CH2CH3 Ethyl ethanoate Ethyl acetate

Acid Halide H3CCOCl Ethanoyl chloride Acetyl chloride

Amide H3CCON(CH3)2 N,N-Dimethylethanamide N,N-Dimethylacetamide

Acid Anhydride (H3CCO)2O Ethanoic anhydride Acetic anhydride

EXERCISES
QUESTIONS
Q3.1.1
The following is the molecule for ATP, or the molecule responsible for energy in human cells. Identify the functional groups for ATP.

SOLUTIONS
S3.1.1

3.2.7 Updated 7/7/2019

CONTRIBUTORS
Dr. Dietmar Kennepohl FCIC (Professor of Chemistry, Athabasca University)
Prof. Steven Farmer (Sonoma State University)
Organic Chemistry With a Biological Emphasis by Tim Soderberg (University of Minnesota, Morris)

3.2.8 Updated 7/7/2019

3.3: ALKANES AND ALKANE ISOMERS
OBJECTIVES
After completing this section, you should be able to
1. draw the Kekulé structure, condensed structure and shorthand structure of each of the first ten straight-chain alkanes.
2. name each of the first ten straight-chain alkanes, given its molecular formula, Kekulé structure, condensed structure or
shorthand structure.
3. explain the difference in structure between a straight- and a branched-chain alkane, and illustrate the difference using a suitable
example.
4. explain why the number of possible isomers for a given molecular formula increases as the number of carbon atoms increases.
5. draw all the possible isomers that correspond to a given molecular formula of the type Cn H2n+2, where n is ≤ 7.

KEY TERMS
Make certain that you can define, and use in context, the key terms below.
branched-chain alkane
constitutional or structural isomer
homologous series
isomer
saturated hydrocarbon
straight-chain alkane (or normal alkane)

STUDY NOTES
A series of compounds in which successive members differ from one another by a CH2 unit is called a homologous series. Thus, the
series CH4, C2H6, C3H8 . . . CnH2n+2, is an example of a homologous series.
It is important that you commit to memory the names of the first 10 straight-chain alkanes (i.e., from CH4 to C10H22). You will use
these names repeatedly when you begin to learn how to derive the systematic names of a large variety of organic compounds. You
need not remember the number of isomers possible for alkanes containing more than seven carbon atoms. Such information is
available in reference books when it is needed. When drawing isomers, be careful not to deceive yourself into thinking that you can
draw more isomers than you are supposed to be able to. Remember that it is possible to draw each isomer in several different ways
and you may inadvertently count the same isomer more than once.

Alkanes are organic compounds that consist entirely of single-bonded carbon and hydrogen atoms and lack any other functional
groups. Alkanes have the general formula C H n and can be subdivided into the following three groups: the linear straight-chain
2n+2

alkanes, branched alkanes, and cycloalkanes. Alkanes are also saturated hydrocarbons.
Cycloalkanes are cyclic hydrocarbons, meaning that the carbons of the molecule are arranged in the form of a ring. Cycloalkanes are
also saturated, meaning that all of the carbons atoms that make up the ring are single bonded to other atoms (no double or triple bonds).
There are also polycyclic alkanes, which are molecules that contain two or more cycloalkanes that are joined, forming multiple rings.
This is an introductory page about alkanes, such as methane, ethane, propane, butane and the remainder of the common alkanes. This
page addresses their formulae and isomerism, their physical properties, and an introduction to their chemical reactivity.

MOLECULAR FORMULAS
Alkanes are the simplest family of hydrocarbons - compounds containing carbon and hydrogen only. Alkanes only contain carbon-
hydrogen bonds and carbon-carbon single bonds. The first six alkanes are as follows:
methane CH4
ethane C2H6
propane C3H8
butane C4H10
pentane C5H12
hexane C6H14

You can work out the formula of any of the alkanes using the general formula CnH2n+2

ISOMERISM

3.3.1 Updated 7/7/2019

All of the alkanes containing 4 or more carbon atoms show structural isomerism, meaning that there are two or more different
structural formulae that you can draw for each molecular formula.

EXAMPLE: BUTANE OR METHYLPROPANE

C4H10 could be either of these two different molecules:

These are named butane and 2-methylpropane, respectively

WHAT IS STRUCTURAL ISOMERISM?

Isomers are molecules that have the same molecular formula, but have a different arrangement of the atoms in space. That excludes any
different arrangements which are simply due to the molecule rotating as a whole, or rotating about particular bonds. For example, both
of the following are the same molecule. They are not isomers; both are butane.

There are also endless other possible ways that this molecule could twist itself. There is completely free rotation around all the carbon-
carbon single bonds. If you had a model of a molecule in front of you, you would have to take it to pieces and rebuild it if you wanted
to make an isomer of that molecule. If you can make an apparently different molecule just by rotating single bonds, it's not different -
it's still the same molecule.
In structural isomerism, the atoms are arranged in a completely different order. This is easier to see with specific examples. What
follows looks at some of the ways that structural isomers can arise. The names of the various forms of structural isomerism probably
do not matter all that much, but you must be aware of the different possibilities when you come to draw isomers.

CHAIN ISOMERISM
These isomers arise because of the possibility of branching in carbon chains. For example, there are two isomers of butane, C4H10. In
one of them, the carbon atoms lie in a "straight chain" whereas in the other the chain is branched.

Be careful not to draw "false" isomers which are just twisted versions of the original molecule. For example, this structure is just the
straight chain version of butane rotated about the central carbon-carbon bond.

You could easily see this with a model. This is the example we've already used at the top of this page.

EXAMPLE 3.3.1 : CHAIN ISOMERS IN PENTANE

Pentane, C5H12, has three chain isomers. If you think you can find any others, they are simply twisted versions of the ones below. If
in doubt make some models.

3.3.2 Updated 7/7/2019

EXERCISES
QUESTIONS
Q3.2.1
Give all the isomers for a straight chain hexanol.
SOLUTIONS
S3.2.1

CONTRIBUTORS
Dr. Dietmar Kennepohl FCIC (Professor of Chemistry, Athabasca University)
Prof. Steven Farmer (Sonoma State University)
Organic Chemistry With a Biological Emphasis by Tim Soderberg (University of Minnesota, Morris)

3.3.3 Updated 7/7/2019

3.4: ALKYL GROUPS
OBJECTIVES
After completing this section, you should be able to
1. recognize and name any alkyl group that can be considered to have been formed by the removal of a terminal hydrogen atom
from a straight-chain alkane containing ten or fewer carbon atoms.
2. explain what is meant by a primary, secondary, tertiary or quaternary carbon atom.
3. represent the various types of organic compounds using the symbol “R” to represent any alkyl group.

KEY TERMS
Make certain that you can define, and use in context, the key terms below.
alkyl group
methyl group
primary carbon
quaternary carbon
secondary carbon
tertiary carbon

STUDY NOTES
The differences among primary, secondary, tertiary and quaternary carbon atoms are explained in the following discussion. A
convenient way of memorizing this classification scheme is to remember that a primary carbon atom is attached directly to only one
other carbon atom, a secondary carbon atom is attached directly to two carbon atoms, and so on.

The IUPAC system requires first that we have names for simple unbranched chains, as noted above, and second that we have names
for simple alkyl groups that may be attached to the chains. Examples of some common alkyl groups are given in the following table.
Note that the "ane" suffix is replaced by "yl" in naming groups. The symbol R is used to designate a generic (unspecified) alkyl group.
Table 3.4.1: Alkyl Group names
Group CH3– C2H5– CH3CH2CH2– (CH3)2CH– CH3CH2CH2CH2– (CH3)2CHCH2– CH3CH2CH(CH3)– (CH3)3C– R–
Name Methyl Ethyl Propyl Isopropyl Butyl Isobutyl sec-Butyl tert-Butyl Alkyl

ALKYL GROUPS
Alkanes can be described by the general formula CnH2n+2. An alkyl group is formed by removing one hydrogen from the alkane chain
and is described by the formula CnH2n+1. The removal of this hydrogen results in a stem change from -ane to -yl. Take a look at the
following examples.

The same concept can be applied to any of the straight chain alkane names provided in Table 3.4.2.

3.4.1 Updated 7/7/2019

 Table 3.4.2: straight chain alkane
Name Molecular Formula Condensed Structural Formula
Methane CH4 CH4

Ethane C2H6 CH3CH3

Propane C3H8 CH3CH2CH3

Butane C4H10 CH3(CH2)2CH3

Pentane C5H12 CH3(CH2)3CH3

Hexane C6H14 CH3(CH2)4CH3

Heptane C7H16 CH3(CH2)5CH3

Octane C8H18 CH3(CH2)6CH3

Nonane C9H20 CH3(CH2)7CH3

Decane C10H22 CH3(CH2)8CH3

Undecane C11H24 CH3(CH2)9CH3

Dodecane C12H26 CH3(CH2)10CH3

Tridecane C13H28 CH3(CH2)11CH3

Tetradecane C14H30 CH3(CH2)12CH3

Pentadecane C15H32 CH3(CH2)13CH3

Hexadecane C16H34 CH3(CH2)14CH3

Heptadecane C17H36 CH3(CH2)15CH3

Octadecane C18H38 CH3(CH2)16CH3

Nonadecane C19H40 CH3(CH2)17CH3

Eicosane C20H42 CH3(CH2)18CH3

CLASSIFICATION OF CARBON ATOMS

Carbons have a special terminology to describe how many other carbons they are attached to.

Primary carbons (1o) attached to one other C atom

Secondary carbons (2o) are attached to two other C’s
Tertiary carbons (3o) are attached to three other C’s
Quaternary carbons (4o) are attached to four C's

EXAMPLE 3.4.1
You will find that hydrogen atoms are also classified in this manner. A hydrogen atom attached to a primary carbon atom is called a
primary hydrogen; thus, isobutane, has nine primary hydrogens and one tertiary hydrogen.

3.4.2 Updated 7/7/2019

 Primary hydrogens (1o) are attached to carbons bonded to one other C atom
Secondary hydrogens (2o) are attached to carbons bonded to two other C’s
Tertiary hydrogens (3o) are attached to carbons bonded to three other C’s

EXAMPLE 3.4.2

EXERCISES
QUESTIONS
Q3.3.1
Consider the following molecule. How many carbons are in the longest chain? Find a primary and quaternary carbon, and label an
ethyl group.
SOLUTIONS
S3.3.1

A = 4° Carbon
B = Ethyl Group
C = 1° Carbon
The longest chain is 10 carbons long

3.4.3 Updated 7/7/2019

CONTRIBUTORS
Dr. Dietmar Kennepohl FCIC (Professor of Chemistry, Athabasca University)
Prof. Steven Farmer (Sonoma State University)
William Reusch, Professor Emeritus (Michigan State U.), Virtual Textbook of Organic Chemistry
Organic Chemistry With a Biological Emphasis by Tim Soderberg (University of Minnesota, Morris)

3.4.4 Updated 7/7/2019

3.5: NAMING ALKANES
OBJECTIVES
After completing this section, you should be able to
1. provide the correct IUPAC name for any given alkane structure (Kekulé, condensed or shorthand).
2. draw the Kekulé, condensed or shorthand structure of an alkane, given its IUPAC name.

KEY TERMS
Make certain that you can define, and use in context, the key term below.
IUPAC system

STUDY NOTES
The IUPAC system of nomenclature aims to ensure
1. that every organic compound has a unique, unambiguous name.
2. that the IUPAC name of any compound conveys the structure of that compound to a person familiar with the system.
One way of checking whether the name you have given to an alkane is reasonable is to count the number of carbon atoms implied by the chosen name. For example, if you named a compound 3‑ethyl-
4‑methylheptane, you have indicated that the compound contains a total of 10 carbon atoms—seven carbon atoms in the main chain, two carbon atoms in an ethyl group, and one carbon atom in a
methyl group. If you were to check the given structure and find 11 carbon atoms, you would know that you had made a mistake. Perhaps the name you should have written was 3‑ethyl-
4,4‑dimethylheptane!
When naming alkanes, a common error of beginning students is a failure to pick out the longest carbon chain. For example, the correct name for the compound shown below is 3‑methylheptane, not
2‑ethylhexane.

Remember that every substituent must have a number, and do not forget the prefixes: di, tri, tetra, etc.
You must use commas to separate numbers, and hyphens to separate numbers and substituents. Notice that 3‑methylhexane is one word.

Hydrocarbons having no double or triple bond functional groups are classified as alkanes or cycloalkanes, depending on whether the carbon atoms of the molecule are arranged only in chains or also in
rings. Although these hydrocarbons have no functional groups, they constitute the framework on which functional groups are located in other classes of compounds, and provide an ideal starting point for
studying and naming organic compounds. The alkanes and cycloalkanes are also members of a larger class of compounds referred to as aliphatic. Simply put, aliphatic compounds are compounds that do
not incorporate any aromatic rings in their molecular structure.
The following table lists the IUPAC names assigned to simple continuous-chain alkanes from C-1 to C-10. A common "ane" suffix identifies these compounds as alkanes. Longer chain alkanes are well
known, and their names may be found in many reference and text books. The names methane through decane should be memorized, since they constitute the root of many IUPAC names. Fortunately,
common numerical prefixes are used in naming chains of five or more carbon atoms.
Table 3.5.1: Simple Unbranched Alkanes
Na Molecular Structural Isomers Name Molecular Structural Iso
me Formula Formula Formula Formula me
rs
me CH4 CH4 1 hexane C6H14 CH3(CH2)4CH3 5
tha
ne
eth C2H6 CH3CH3 1 heptane C7H16 CH3(CH2)5CH3 9
an
e
pro C3H8 CH3CH2CH3 1 octane C8H18 CH3(CH2)6CH3 18
pa
ne
but C4H10 CH3CH2CH2CH3 2 nonane C9H20 CH3(CH2)7CH3 35
an
e
pe C5H12 CH3(CH2)3CH3 3 decane C10H22 CH3(CH2)8CH3 75
nta
ne

SOME IMPORTANT BEHAVIOR TRENDS AND TERMINOLOGIES

1. The formulas and structures of these alkanes increase uniformly by a CH2 increment.
2. A uniform variation of this kind in a series of compounds is called homologous.
3. These formulas all fit the CnH2n+2 rule. This is also the highest possible H/C ratio for a stable hydrocarbon.
4. Since the H/C ratio in these compounds is at a maximum, we call them saturated (with hydrogen).

Beginning with butane (C4H10), and becoming more numerous with larger alkanes, we note the existence of alkane isomers. For example, there are five C6H14 isomers, shown below as abbreviated line
formulas (A through E):

Although these distinct compounds all have the same molecular formula, only one (A) can be called hexane. How then are we to name the others?
The IUPAC system requires first that we have names for simple unbranched chains, as noted above, and second that we have names for simple alkyl groups that may be attached to the chains. Examples of
some common alkyl groups are given in the following table. Note that the "ane" suffix is replaced by "yl" in naming groups. The symbol R is used to designate a generic (unspecified) alkyl group.
Table 3.5.2: Alkyl Groups Names
Group CH3– C2H5– CH3CH2CH2– (CH3)2CH– CH3CH2CH
(CH
2CH
3)22CHCH
– 2– CH3CH2CH(CH3)– (CH3)3C–
Name Methyl Ethyl Propyl Isopropyl B Isobutyl sec-Butyl tert-Butyl
u
t
y
l

IUPAC RULES FOR ALKANE NOMENCLATURE

1. Find and name the longest continuous carbon chain.
2. Identify and name groups attached to this chain.
3. Number the chain consecutively, starting at the end nearest a substituent group.
4. Designate the location of each substituent group by an appropriate number and name.
5. Assemble the name, listing groups in alphabetical order.
6. The prefixes di, tri, tetra etc., used to designate several groups of the same kind, are not considered when alphabetizing.

3.5.1 Updated 7/7/2019

Halogen substituents are easily accommodated, using the names: fluoro (F-), chloro (Cl-), bromo (Br-) and iodo (I-).

EXAMPLE 3.5.1 : HALOGEN SUBSTITUTION

For example, (CH3)2CHCH2CH2Br would be named 1-bromo-3-methylbutane. If the halogen is bonded to a simple alkyl group an alternative "alkyl halide" name may be used. Thus, C2H5Cl may be
named chloroethane (no locator number is needed for a two carbon chain) or ethyl chloride.
For the above isomers of hexane the IUPAC names are: B 2-methylpentane C 3-methylpentane D 2,2-dimethylbutane E 2,3-dimethylbutane

ALKYL GROUPS
Alkanes can be described by the general formula CnH2n+2. An alkyl group is formed by removing one hydrogen from the alkane chain and is described by the formula CnH2n+1. The removal of this
hydrogen results in a stem change from -ane to -yl. Take a look at the following examples.

The same concept can be applied to any of the straight chain alkane names provided in the table above.
Name Molecular Formula Condensed Structural Formula
Methane CH4 CH4

Ethane C2H6 CH3CH3

Propane C3H8 CH3CH2CH3

Butane C4H10 CH3(CH2)2CH3

Pentane C5H12 CH3(CH2)3CH3

Hexane C6H14 CH3(CH2)4CH3

Heptane C7H16 CH3(CH2)5CH3

Octane C8H18 CH3(CH2)6CH3

Nonane C9H20 CH3(CH2)7CH3

Decane C10H22 CH3(CH2)8CH3

Undecane C11H24 CH3(CH2)9CH3

Dodecane C12H26 CH3(CH2)10CH3

Tridecane C13H28 CH3(CH2)11CH3

Tetradecane C14H30 CH3(CH2)12CH3

Pentadecane C15H32 CH3(CH2)13CH3

Hexadecane C16H34 CH3(CH2)14CH3

Heptadecane C17H36 CH3(CH2)15CH3

Octadecane C18H38 CH3(CH2)16CH3

Nonadecane C19H40 CH3(CH2)17CH3

Eicosane C20H42 CH3(CH2)18CH3

THREE RULES OF NAMING ALKANES

1. Choose the longest, most substituted carbon chain containing a functional group.
2. A carbon bonded to a functional group must have the lowest possible carbon number. If there are no functional groups, then any substitute present must have the lowest possible number.
3. Take the alphabetical order into consideration; that is, after applying the first two rules given above, make sure that your substitutes and/or functional groups are written in alphabetical order.

EXAMPLE 3.5.2
What is the name of the follow molecule?

SOLUTION
Rule #1: Choose the longest, most substituted carbon chain containing a functional group. This example does not contain any functional groups, so we only need to be concerned with choosing the
longest, most substituted carbon chain. The longest carbon chain has been highlighted in red and consists of eight carbons.

Rule #2: Carbons bonded to a functional group must have the lowest possible carbon number. If there are no functional groups, then any substitute present must have the lowest possible number.
Because this example does not contain any functional groups, we only need to be concerned with the two substitutes present, that is, the two methyl groups. If we begin numbering the chain from the
left, the methyls would be assigned the numbers 4 and 7, respectively. If we begin numbering the chain from the right, the methyls would be assigned the numbers 2 and 5. Therefore, to satisfy the
second rule, numbering begins on the right side of the carbon chain as shown below. This gives the methyl groups the lowest possible numbering.

3.5.2 Updated 7/7/2019

Rule 3: In this example, there is no need to utilize the third rule. Because the two substitutes are identical, neither takes alphabetical precedence with respect to numbering the carbons. This concept will
become clearer in the following examples.
The name of this molecule is thus: 2,5-dimethyloctane

EXAMPLE 3.5.3
What is the name of the follow molecule?

SOLUTION
Rule #1: Choose the longest, most substituted carbon chain containing a functional group. This example contains two functional groups, bromine and chlorine. The longest carbon chain has been
highlighted in red and consists of seven carbons.

Rule #2: Carbons bonded to a functional group must have the lowest possible carbon number. If there are no functional groups, then any substitute present must have the lowest possible number. In this
example, numbering the chain from the left or the right would satisfy this rule. If we number the chain from the left, bromine and chlorine would be assigned the second and sixth carbon positions,
respectively. If we number the chain from the right, chlorine would be assigned the second position and bromine would be assigned the sixth position. In other words, whether we choose to number from
the left or right, the functional groups occupy the second and sixth positions in the chain. To select the correct numbering scheme, we need to utilize the third rule.

Rule #3: After applying the first two rules, take the alphabetical order into consideration. Alphabetically, bromine comes before chlorine. Therefore, bromine is assigned the second carbon position, and
chlorine is assigned the sixth carbon position.

The name of this molecule is thus: 2-bromo-6-chloroheptane

EXAMPLE 3.5.4
What is the name of the follow molecule?

SOLUTION
Rule #1: Choose the longest, most substituted carbon chain containing a functional group. This example contains two functional groups, bromine and chlorine, and one substitute, the methyl group. The
longest carbon chain has been highlighted in red and consists of seven carbons.

Rule #2: Carbons bonded to a functional group must have the lowest possible carbon number. After taking functional groups into consideration, any substitutes present must have the lowest possible
carbon number. This particular example illustrates the point of difference principle. If we number the chain from the left, bromine, the methyl group and chlorine would occupy the second, fifth and
sixth positions, respectively. This concept is illustrated in the second drawing below. If we number the chain from the right, chlorine, the methyl group and bromine would occupy the second, third and
sixth positions, respectively, which is illustrated in the first drawing below. The position of the methyl, therefore, becomes a point of difference. In the first drawing, the methyl occupies the third
position. In the second drawing, the methyl occupies the fifth position. To satisfy the second rule, we want to choose the numbering scheme that provides the lowest possible numbering of this substitute.
Therefore, the first of the two carbon chains shown below is correct.

Therefore, the first numbering scheme is the appropriate one to use.

Once you have determined the correct numbering of the carbons, it is often useful to make a list, including the functional groups, substitutes, and the name of the parent chain.
Rule #3: After applying the first two rules, take the alphabetical order into consideration. Alphabetically, bromine comes before chlorine. Therefore, bromine is assigned the second carbon position, and
chlorine is assigned the sixth carbon position.
Parent chain: heptane 2-Chloro 3-Methyl 6-Bromo

3.5.3 Updated 7/7/2019

 6-bromo-2-chloro-3-methylheptane

EXERCISES
3.4 EXERCISES
QUESTIONS
Q3.4.1
Are the following structures properly named, and if they are not, what is the correct naming?

Q3.4.2
Give the name of the following molecules:

SOLUTIONS
S3.4.1
They are both labeled incorrectly:
3-bromo-2-hydroxypentane
2, 3-dimethylpentane
S3.4.2
1 = 3,4-Dimethyl hexane
2 = 2-methyl pentane
3 = 2,2,4-trimethyl pentane

CONTRIBUTORS
Dr. Dietmar Kennepohl FCIC (Professor of Chemistry, Athabasca University)
Prof. Steven Farmer (Sonoma State University)
Organic Chemistry With a Biological Emphasis by Tim Soderberg (University of Minnesota, Morris)

3.5.4 Updated 7/7/2019

3.6: PROPERTIES OF ALKANES
OBJECTIVES
After completing this section, you should be able to
1. arrange a number of given straight-chain alkanes in order of increasing or decreasing boiling point or melting point.
2. arrange a series of isomeric alkanes in order of increasing or decreasing boiling point.
3. explain the difference in boiling points between a given number of alkanes.

KEY TERMS
Make certain that you can define, and use in context, the key term below.
van der Waals force

Alkanes are not very reactive and have little biological activity; all alkanes are colorless and odorless.

BOILING POINTS
The boiling points shown are for the "straight chain" isomers of which there is more than one. The first four alkanes are gases at room
temperature, and solids do not begin to appear until about C H , but this is imprecise because different isomers typically have
17 36

different melting and boiling points. By the time you get 17 carbons into an alkane, there are unbelievable numbers of isomers!

Cycloalkanes have boiling points that are approximately 20 K higher than the corresponding straight chain alkane.
There is not a significant electronegativity difference between carbon and hydrogen, thus, there is not any significant bond polarity.
The molecules themselves also have very little polarity. A totally symmetrical molecule like methane is completely non-polar, meaning
that the only attractions between one molecule and its neighbors will be Van der Waals dispersion forces. These forces will be very
small for a molecule like methane but will increase as the molecules get bigger. Therefore, the boiling points of the alkanes increase
with molecular size.
Where you have isomers, the more branched the chain, the lower the boiling point tends to be. Van der Waals dispersion forces are
smaller for shorter molecules and only operate over very short distances between one molecule and its neighbors. It is more difficult
for short, fat molecules (with lots of branching) to lie as close together as long, thin molecules.

EXAMPLE 3.5.1: BOILING POINTS OF ALKANES

For example, the boiling points of the three isomers of C 5 H12 are:
pentane: 309.2 K
2-methylbutane: 301.0 K
2,2-dimethylpropane: 282.6 K
The slightly higher boiling points for the cycloalkanes are presumably because the molecules can get closer together because the
ring structure makes them tidier and less "wriggly"!

EXERCISE 3.5.1
For each of the following pairs of compounds, select the substance which you expect to have the higher boiling point:
a. octane and nonane.
b. octane and 2,2,3,3-tetramethylbutane.

3.6.1 Updated 7/7/2019

SOLUBILITY
Alkanes are virtually insoluble in water, but dissolve in organic solvents. However, liquid alkanes are good solvents for many other
non-ionic organic compounds.
SOLUBILITY IN WATER
When a molecular substance dissolves in water, the following must occur:
break the intermolecular forces within the substance. In the case of the alkanes, these are the Van der Waals dispersion forces.
break the intermolecular forces in the water so that the substance can fit between the water molecules. In water, the primary
intermolecular attractions are hydrogen bonds.
Breaking either of these attractions requires energy, although the amount of energy to break the Van der Waals dispersion forces in
something like methane is relatively negligible; this is not true of the hydrogen bonds in water.
As something of a simplification, a substance will dissolve if there is enough energy released when new bonds are made between the
substance and the water to compensate for what is used in breaking the original attractions. The only new attractions between the
alkane and the water molecules are Van der Waals forces. These forces do not release a sufficient amount of energy to compensate for
the energy required to break the hydrogen bonds in water. The alkane does not dissolve.

NOTE
This is a simplification because entropic effects are important when things dissolve.

SOLUBILITY IN ORGANIC SOLVENTS

In most organic solvents, the primary forces of attraction between the solvent molecules are Van der Waals - either dispersion forces or
dipole-dipole attractions. Therefore, when an alkane dissolves in an organic solvent, the Van der Waals forces are broken and are
replaced by new Van der Waals forces. The two processes more or less cancel each other out energetically; thus, there is no barrier to
solubility.

EXERCISES
1. For each of the following pairs of compounds, select the substance you expect to have the higher boiling point.
a. octane and nonane.
b. octane and 2,2,3,3‑tetramethylbutane.

ANSWERS:
a. Nonane will have a higher boiling point than octane, because it has a longer carbon chain than octane.
b. Octane will have a higher boiling point than 2,2,3,3‑tetramethylbutane, because it branches less than 2,2,3,3‑tetramethylbutane, and
therefore has a larger “surface area” and more van der Waals forces.
Note: The actual boiling points are
nonane, 150.8°C
octane, 125.7°C
2,2,3,3‑tetramethylbutane, 106.5°C

CONTRIBUTORS
Dr. Dietmar Kennepohl FCIC (Professor of Chemistry, Athabasca University)
Prof. Steven Farmer (Sonoma State University)
Jim Clark (Chemguide.co.uk)

3.6.2 Updated 7/7/2019

3.7: CONFORMATIONS OF ETHANE
OBJECTIVES
After completing this section, you should be able to
1. explain the concept of free rotation about a carbon-carbon single bond.
2. explain the difference between conformational isomerism and the other types of isomerism which you have encountered.
3. represent the conformers of ethane by both sawhorse representation and Newman projection.
4. sketch a graph of energy versus bond rotation for ethane, and discuss the graph in terms of torsional strain.

KEY TERMS
Make certain that you can define, and use in context, the key terms below.
conformation (conformer, conformational isomer)
eclipsed conformation
Newman projection
sawhorse representation
staggered conformation
strain energy
torsional strain (eclipsing strain)

STUDY NOTES
You should be prepared to sketch various conformers using both sawhorse representations and Newman projections. Each method
has its own advantages, depending upon the circumstances. Notice that when drawing the Newman projection of the eclipsed
conformation of ethane, you cannot draw the rear hydrogens exactly behind the front ones. This is an inherent limitation associated
with representing a 3-D structure in two dimensions.

Conformational isomerism involves rotation about sigma bonds, and does not involve any differences in the connectivity or geometry
of bonding. Two or more structures that are categorized as conformational isomers, or conformers, are really just two of the exact
same molecule that differ only in terms of the angle about one or more sigma bonds.

ETHANE CONFORMATIONS
Although there are seven sigma bonds in the ethane molecule, rotation about the six carbon-hydrogen bonds does not result in any
change in the shape of the molecule because the hydrogen atoms are essentially spherical. Rotation about the carbon-carbon bond,
however, results in many different possible molecular conformations.

In order to better visualize these different conformations, it is convenient to use a drawing convention called the Newman projection.
In a Newman projection, we look lengthwise down a specific bond of interest – in this case, the carbon-carbon bond in ethane. We
depict the ‘front’ atom as a dot, and the ‘back’ atom as a larger circle.

The six carbon-hydrogen bonds are shown as solid lines protruding from the two carbons at 120°angles, which is what the actual
tetrahedral geometry looks like when viewed from this perspective and flattened into two dimensions.
The lowest energy conformation of ethane, shown in the figure above, is called the ‘staggered’ conformation, in which all of the C-H
bonds on the front carbon are positioned at dihedral angles of 60°relative to the C-H bonds on the back carbon. In this conformation,
the distance between the bonds (and the electrons in them) is maximized.

3.7.1 Updated 7/7/2019

If we now rotate the front CH3 group 60° clockwise, the molecule is in the highest energy ‘eclipsed' conformation, where the
hydrogens on the front carbon are as close as possible to the hydrogens on the back carbon.

This is the highest energy conformation because of unfavorable interactions between the electrons in the front and back C-H bonds.
The energy of the eclipsed conformation is approximately 3 kcal/mol higher than that of the staggered conformation. Another
60°rotation returns the molecule to a second eclipsed conformation. This process can be continued all around the 360°circle, with three
possible eclipsed conformations and three staggered conformations, in addition to an infinite number of variations in between.

UNHINDERED (FREE) ROTATIONS DO NOT EXIST IN ETHANE

The carbon-carbon bond is not completely free to rotate – there is indeed a small, 3 kcal/mol barrier to rotation that must be overcome
for the bond to rotate from one staggered conformation to another. This rotational barrier is not high enough to prevent constant
rotation except at extremely cold temperatures. However, at any given moment the molecule is more likely to be in a staggered
conformation - one of the rotational ‘energy valleys’ - than in any other state. The potential energy associated with the various
conformations of ethane varies with the dihedral angle of the bonds, as shown below.

Figure 3.6.X: The potential energy associated with the various conformations of ethane varies with the dihedral angle of the bonds.
Newman projections of butane conformations & their relative energy differences (not total energies). Conformations form when butane
rotates about one of its single covalent bond. Torsional/dihedral angle is shown on x-axis. Conformations (according to IUPAC): A:
antiperiplanar, anti or trans B: synclinal or gauche C: anticlinal or eclipsed D: synperiplanar or cis Valleys of the pink graph are
conformations lowest in energy (shown as A & B). Peaks are conformations highest in energy (shown as C & D). Energies are
A<B<C<D with D highest & A lowest in energy. A is thus the most stable conformation &, of all the other conformations, occurs most
often in room temperature. Valleys A & B are local energy minima & A is global minima. A & B can thus be classified as rotamers (a
class of conformers). Peaks are not rotamers, & are caused by repulsive forces of the hydrogens & methyls (-CH3). Source for
conformation names & conformer classification: Pure & Appl. Chem., Vol. 68, No. 12, pp. 2193-2222, 1996 Image used with
permission (Public Domain; Keministi).
Although the conformers of ethane are in rapid equilibrium with each other, the 3 kcal/mol energy difference leads to a substantial
preponderance of staggered conformers (> 99.9%) at any given time. The animation below illustrates the relationship between ethane's
potential energy and its dihedral angle

3.7.2 Updated 7/7/2019

 Figure 3.6.X: Animation of potential energy vs. dihedral angle in ethane

EXERCISES
QUESTIONS
Q3.6.1
What is the most stable rotational conformation of ethane and explain why it is preferred over the other conformation?
SOLUTIONS
S3.6.1
Staggered, as there is less repulsion between the hydrogen atoms.

CONTRIBUTORS
William Reusch, Professor Emeritus (Michigan State U.), Virtual Textbook of Organic Chemistry
Dr. Dietmar Kennepohl FCIC (Professor of Chemistry, Athabasca University)

3.7.3 Updated 7/7/2019

3.8: CONFORMATIONS OF OTHER ALKANES
OBJECTIVES
After completing this section, you should be able to
1. depict the staggered and eclipsed conformers of propane (or a similar compound) using sawhorse representations and Newman
projections.
2. sketch a graph of energy versus bond rotation for propane (or a similar compound) and discuss the graph in terms of torsional
strain.
3. depict the anti, gauche, eclipsed and fully eclipsed conformers of butane (or a similar compound), using sawhorse
representations and Newman projections.
4. sketch a graph of energy versus ($\ce{\sf{C{2}-C{3}}}$) bond rotation for butane (or a similar compound), and discuss it in
terms of torsional and steric repulsion.
5. assess which of two (or more) conformers of a given compound is likely to predominate at room temperature from a semi-
quantitative knowledge of the energy costs of the interactions involved.

KEY TERMS
Make certain that you can define, and use in context, the key terms below.
anti conformation
gauche conformation
eclipsed conformation
steric repulsion

In butane, there are now three rotating carbon-carbon bonds to consider, but we will focus on the middle bond between C2 and C3.
Below are two representations of butane in a conformation which puts the two CH3 groups (C1 and C4) in the eclipsed position.

This is the highest energy conformation for butane, due to what is called ‘van der Waals repulsion’, or ‘steric repulsion’, between
the two rather bulky methyl groups.
What is van der Waals repulsion? Didn’t we just learn in Chapter 2 that the van der Waals force between two nonpolar groups is an
attractive force? Consider this: you probably like to be near your friends, but no matter how close you are you probably don’t want to
share a one-room apartment with five of them. When the two methyl groups are brought too close together, the overall resulting
noncovalent interaction is repulsive rather than attractive. The result is that their respective electron densities repel one another.
If we rotate the front, (blue) carbon by 60°clockwise, the butane molecule is now in a staggered conformation.

This is more specifically referred to as the ‘gauche’ conformation of butane. Notice that although they are staggered, the two methyl
groups are not as far apart as they could possibly be. There is still significant steric repulsion between the two bulky groups. A further
rotation of 60°gives us a second eclipsed conformation (B) in which both methyl groups are lined up with hydrogen atoms.

3.8.1 Updated 7/7/2019

Due to steric repulsion between methyl and hydrogen substituents, this eclipsed conformation B is higher in energy than the gauche
conformation. However, because there is no methyl-to-methyl eclipsing, it is lower in energy than eclipsed conformation A. One more
60 rotation produces the ‘anti’ conformation, where the two methyl groups are positioned opposite each other and steric repulsion is
minimized.

This is the lowest energy conformation for butane. The diagram below summarizes the relative energies for the various eclipsed,
staggered, and gauche conformations.

At room temperature, butane is most likely to be in the lowest-energy anti conformation at any given moment in time, although the
energy barrier between the anti and eclipsed conformations is not high enough to prevent constant rotation except at very low
temperatures. For this reason (and also simply for ease of drawing), it is conventional to draw straight-chain alkanes in a zigzag form,
which implies anti conformation at all carbon-carbon bonds.

EXAMPLE 3.8.1
Draw Newman projections of the eclipsed and staggered conformations of propane.

Answer:

3.8.2 Updated 7/7/2019

 EXAMPLE 3.8.2
Draw a Newman projection, looking down the C2-C3 bond, of 1-butene in the conformation shown below.

Answer:

The following diagram illustrates the change in potential energy that occurs with rotation about the C2–C3 bond.

Figure 3.8.2: Potential curve vs dihedral angle of the C2-C3 bond of butane.

EXERCISES
QUESTIONS
Q3.7.1
Draw the energy diagram for the rotation of the bond highlighted in pentane.

SOLUTIONS
S3.7.1

3.8.3 Updated 7/7/2019

CONTRIBUTORS
Dr. Dietmar Kennepohl FCIC (Professor of Chemistry, Athabasca University)
Prof. Steven Farmer (Sonoma State University)
Organic Chemistry With a Biological Emphasis by Tim Soderberg (University of Minnesota, Morris)
Jim Clark (Chemguide.co.uk)
William Reusch, Professor Emeritus (Michigan State U.), Virtual Textbook of Organic Chemistry

3.8.4 Updated 7/7/2019

3.9: GASOLINE - A DEEPER LOOK
OBJECTIVES
After completing this section, you should be able to
1. describe the general nature of petroleum deposits, and recognize why petroleum is such an important source of organic
compounds.
2. explain, in general terms, the processes involved in the refining of petroleum.
3. define the octane number of a fuel, and relate octane number to chemical structure.

KEY TERMS
Make certain that you can define, and use in context, the key terms below.
catalytic cracking
catalytic reforming
fractional distillation
octane number (octane rating)

STUDY NOTES
The refining of petroleum into usable fractions is a very important industrial process. In the laboratory component of this course,
you will have the opportunity to compare this industrial process to the procedure as it is performed in the laboratory.

PETROLEUM
The petroleum that is pumped out of the ground at locations around the world is a complex mixture of several thousand organic
compounds, including straight-chain alkanes, cycloalkanes, alkenes, and aromatic hydrocarbons with four to several hundred carbon
atoms. The identities and relative abundances of the components vary depending on the source. So Texas crude oil is somewhat
different from Saudi Arabian crude oil. In fact, the analysis of petroleum from different deposits can produce a “fingerprint” of each,
which is useful in tracking down the sources of spilled crude oil. For example, Texas crude oil is “sweet,” meaning that it contains a
small amount of sulfur-containing molecules, whereas Saudi Arabian crude oil is “sour,” meaning that it contains a relatively large
amount of sulfur-containing molecules.

GASOLINE
Petroleum is converted to useful products such as gasoline in three steps: distillation, cracking, and reforming. Recall from Chapter 1
"Introduction to Chemistry" that distillation separates compounds on the basis of their relative volatility, which is usually inversely
proportional to their boiling points. Part (a) in Figure 3.8.1 shows a cutaway drawing of a column used in the petroleum industry for
separating the components of crude oil. The petroleum is heated to approximately 400°C (750°F), at which temperature it has become
a mixture of liquid and vapor. This mixture, called the feedstock, is introduced into the refining tower. The most volatile components
(those with the lowest boiling points) condense at the top of the column where it is cooler, while the less volatile components condense
nearer the bottom. Some materials are so nonvolatile that they collect at the bottom without evaporating at all. Thus the composition of
the liquid condensing at each level is different. These different fractions, each of which usually consists of a mixture of compounds
with similar numbers of carbon atoms, are drawn off separately. Part (b) in Figure 3.8.1 shows the typical fractions collected at
refineries, the number of carbon atoms they contain, their boiling points, and their ultimate uses. These products range from gases used
in natural and bottled gas to liquids used in fuels and lubricants to gummy solids used as tar on roads and roofs.

3.9.1 Updated 7/7/2019

Figure 3.8.1: The Distillation of Petroleum. (a) This is a diagram of a distillation column used for separating petroleum fractions. (b)
Petroleum fractions condense at different temperatures, depending on the number of carbon atoms in the molecules, and are drawn off
from the column. The most volatile components (those with the lowest boiling points) condense at the top of the column, and the least
volatile (those with the highest boiling points) condense at the bottom.
The economics of petroleum refining are complex. For example, the market demand for kerosene and lubricants is much lower than the
demand for gasoline, yet all three fractions are obtained from the distillation column in comparable amounts. Furthermore, most
gasolines and jet fuels are blends with very carefully controlled compositions that cannot vary as their original feedstocks did. To make
petroleum refining more profitable, the less volatile, lower-value fractions must be converted to more volatile, higher-value mixtures
that have carefully controlled formulas. The first process used to accomplish this transformation is cracking, in which the larger and
heavier hydrocarbons in the kerosene and higher-boiling-point fractions are heated to temperatures as high as 900°C. High-temperature
reactions cause the carbon–carbon bonds to break, which converts the compounds to lighter molecules similar to those in the gasoline
fraction. Thus in cracking, a straight-chain alkane with a number of carbon atoms corresponding to the kerosene fraction is converted
to a mixture of hydrocarbons with a number of carbon atoms corresponding to the lighter gasoline fraction. The second process used to
increase the amount of valuable products is called reforming; it is the chemical conversion of straight-chain alkanes to either branched-
chain alkanes or mixtures of aromatic hydrocarbons. Using metals such as platinum brings about the necessary chemical reactions. The
mixtures of products obtained from cracking and reforming are separated by fractional distillation.

OCTANE RATINGS
The quality of a fuel is indicated by its octane rating, which is a measure of its ability to burn in a combustion engine without knocking
or pinging. Knocking and pinging signal premature combustion (Figure 3.8.2), which can be caused either by an engine malfunction or
by a fuel that burns too fast. In either case, the gasoline-air mixture detonates at the wrong point in the engine cycle, which reduces the
power output and can damage valves, pistons, bearings, and other engine components. The various gasoline formulations are designed
to provide the mix of hydrocarbons least likely to cause knocking or pinging in a given type of engine performing at a particular level.

3.9.2 Updated 7/7/2019

 Figure 3.8.2: The Burning of Gasoline in an Internal Combustion Engine. (a) Normally, fuel is ignited by the spark plug, and
combustion spreads uniformly outward. (b) Gasoline with an octane rating that is too low for the engine can ignite prematurely,
resulting in uneven burning that causes knocking and pinging.
The octane scale was established in 1927 using a standard test engine and two pure compounds: n-heptane and isooctane (2,2,4-
trimethylpentane). n-Heptane, which causes a great deal of knocking on combustion, was assigned an octane rating of 0, whereas
isooctane, a very smooth-burning fuel, was assigned an octane rating of 100. Chemists assign octane ratings to different blends of
gasoline by burning a sample of each in a test engine and comparing the observed knocking with the amount of knocking caused by
specific mixtures of n-heptane and isooctane. For example, the octane rating of a blend of 89% isooctane and 11% n-heptane is simply
the average of the octane ratings of the components weighted by the relative amounts of each in the blend. Converting percentages to
decimals, we obtain the octane rating of the mixture:
0.89(100) + 0.11(0) = 89 (3.8.1)

As shown in Figure 3.8.3, many compounds that are now available have octane ratings greater than 100, which means they are better
fuels than pure isooctane. In addition, antiknock agents, also called octane enhancers, have been developed. One of the most widely
used for many years was tetraethyllead [(C2H5)4Pb], which at approximately 3 g/gal gives a 10–15-point increase in octane rating.
Since 1975, however, lead compounds have been phased out as gasoline additives because they are highly toxic. Other enhancers, such
as methyl t-butyl ether (MTBE), have been developed to take their place. They combine a high octane rating with minimal corrosion to
engine and fuel system parts. Unfortunately, when gasoline containing MTBE leaks from underground storage tanks, the result has
been contamination of the groundwater in some locations, resulting in limitations or outright bans on the use of MTBE in certain areas.
As a result, the use of alternative octane enhancers such as ethanol, which can be obtained from renewable resources such as corn,
sugar cane, and, eventually, corn stalks and grasses, is increasing.

Figure 3.8.3: The Octane Ratings of Some Hydrocarbons and Common Additives

CONTRIBUTORS
Dr. Dietmar Kennepohl FCIC (Professor of Chemistry, Athabasca University)

3.9.3 Updated 7/7/2019

4: ORGANIC COMPOUNDS: CYCLOALKANES AND THEIR
STEREOCHEMISTRY

4.1: CHAPTER OBJECTIVES

4.2: NAMING CYCLOALKANES
4.3: CIS-TRANS ISOMERISM IN CYCLOALKANES
4.4: STABILITY OF CYCLOALKANES - RING STRAIN
4.5: CONFORMATIONS OF CYCLOALKANES
4.6: CONFORMATIONS OF CYCLOHEXANE
Rings larger than cyclopentane would have angle strain if they were planar. However, this strain, together with the eclipsing strain
inherent in a planar structure, can be relieved by puckering the ring. Cyclohexane is a good example of a carbocyclic system that
virtually eliminates eclipsing and angle strain by adopting non-planar conformations.

4.7: AXIAL AND EQUATIORIAL BONDS IN CYCLOHEXANE

4.8: CONFORMATIONS OF MONOSUBSTITUTED CYCLOHEXANES
4.9: CONFORMATIONS OF DISUBSTITUTED CYCLOHEXANES
4.10: CONFORMATIONS OF POLYCYCLIC MOLECULES

TOC.1 Updated 7/14/2019

4.1: CHAPTER OBJECTIVES
After you have completed Chapter 4, you should be able to
1. fulfill all of the detailed objectives listed under each individual section.
2. draw the cis-trans isomers of some simple disubstituted cycloalkanes, and write the IUPAC names of such compounds.
3. define, and use in context, the key terms introduced in this chapter.

CONTRIBUTORS
Dr. Dietmar Kennepohl FCIC (Professor of Chemistry, Athabasca University)

4.1.1 Updated 7/7/2019

4.2: NAMING CYCLOALKANES
OBJECTIVES
After completing this section, you should be able to
1. name a substituted or unsubstituted cycloalkane, given its Kekulé structure, shorthand structure or condensed structure.
2. draw the Kekulé, shorthand or condensed structure for a substituted or unsubstituted cycloalkane, given its IUPAC name.
3. draw all possible cycloalkane structures (substituted or unsubstituted) that correspond to a given molecular formula.

STUDY NOTES
Provided that you have mastered the IUPAC system for naming alkanes, you should find that the nomenclature of cycloalkanes does not
present any particular difficulties. Concentrate on the examples in which the substituent or substituents is or are an alkyl group, a
halogen, or both.

Cycloalkanes are cyclic hydrocarbons, meaning that the carbons of the molecule are arranged in the form of a ring. Cycloalkanes are also
saturated, meaning that all of the carbons atoms that make up the ring are single bonded to other atoms (no double or triple bonds). There
are also polycyclic alkanes, which are molecules that contain two or more cycloalkanes that are joined, forming multiple rings.

INTRODUCTION
Many organic compounds found in nature or created in a laboratory contain rings of carbon atoms with distinguishing chemical properties;
these compounds are known as cycloalkanes. Cycloalkanes only contain carbon-hydrogen bonds and carbon-carbon single bonds, but in
cycloalkanes, the carbon atoms are joined in a ring. The smallest cycloalkane is cyclopropane.

Figure 4.1.1:
If you count the carbons and hydrogens, you will see that they no longer fit the general formula C H
n . By joining the carbon atoms in
2n+2

a ring,two hydrogen atoms have been lost. The general formula for a cycloalkane is C H . Cyclic compounds are not all flat molecules.
n 2n

All of the cycloalkanes, from cyclopentane upwards, exist as "puckered rings". Cyclohexane, for example, has a ring structure that looks
like this:

Figure 4.1.2: This is known as the "chair" form of cyclohexane from its shape, which vaguely resembles a chair. Note: The cyclohexane
molecule is constantly changing, with the atom on the left, which is currently pointing down, flipping up, and the atom on the right flipping
down. During this process, another (slightly less stable) form of cyclohexane is formed known as the "boat" form. In this arrangement, both
of these atoms are either pointing up or down at the same time
In addition to being saturated cyclic hydrocarbons, cycloalkanes may have multiple substituents or functional groups that further determine
their unique chemical properties. The most common and useful cycloalkanes in organic chemistry are cyclopentane and cyclohexane,
although other cycloalkanes varying in the number of carbons can be synthesized. Understanding cycloalkanes and their properties are
crucial in that many of the biological processes that occur in most living things have cycloalkane-like structures.

4.2.1 Updated 7/7/2019

 Glucose (6 carbon sugar) Ribose (5 carbon sugar) Cholesterol (polycyclic)

Although polycyclic compounds are important, they are highly complex and typically have common names accepted by IUPAC. However,
the common names do not generally follow the basic IUPAC nomenclature rules. The general formula of the cycloalkanes is C H where
n 2n

n is the number of carbons. The naming of cycloalkanes follows a simple set of rules that are built upon the same basic steps in naming

alkanes. Cyclic hydrocarbons have the prefix "cyclo-".

CONTENTS
For simplicity, cycloalkane molecules can be drawn in the form of skeletal structures in which each intersection between two lines is
assumed to have a carbon atom with its corresponding number of hydrogens.

same as same as
Cycloalkane Molecular Formula Basic Structure
Cyclopropane
C3H6

Cyclobutane
C4H8
Cyclopentane
C5H10

Cyclohexane
C6H12

Cycloheptane
C7H14

Cyclooctane
C8H16

Cyclononane
C9H18

Cyclodecane
C10H20

IUPAC RULES FOR NOMENCLATURE

1. Determine the cycloalkane to use as the parent chain. The parent chain is the one with the highest number of carbon atoms. If there are
two cycloalkanes, use the cycloalkane with the higher number of carbons as the parent chain.
2. If there is an alkyl straight chain that has a greater number of carbons than the cycloalkane, then the alkyl chain must be used as the
primary parent chain. Cycloalkane acting as a substituent to an alkyl chain has an ending "-yl" and, therefore, must be named as a
cycloalkyl.

4.2.2 Updated 7/7/2019

 Cycloalkane Cycloalkyl

cyclopropane cyclopropyl
cyclobutane cyclobutyl
cyclopentane cyclopentyl
cyclohexane cyclohexyl
cycloheptane cycloheptyl
cyclooctane cyclooctyl
cyclononane cyclononanyl
cyclodecane cyclodecanyl

EXAMPLE 4.1.1

The longest straight chain contains 10 carbons, compared with cyclopropane, which only contains 3 carbons. Because cyclopropane is a
substituent, it would be named a cyclopropyl-substituted alkane.

3) Determine any functional groups or other alkyl groups.

4) Number the carbons of the cycloalkane so that the carbons with functional groups or alkyl groups have the lowest possible number. A
carbon with multiple substituents should have a lower number than a carbon with only one substituent or functional group. One way to
make sure that the lowest number possible is assigned is to number the carbons so that when the numbers corresponding to the substituents
are added, their sum is the lowest possible.

(1+3=4) NOT (1+5=6)

5) When naming the cycloalkane, the substituents and functional groups must be placed in alphabetical order.

(ex: 2-bromo-1-chloro-3-methylcyclopentane)
6) Indicate the carbon number with the functional group with the highest priority according to alphabetical order. A dash"-" must be placed
between the numbers and the name of the substituent. After the carbon number and the dash, the name of the substituent can follow. When
there is only one substituent on the parent chain, indicating the number of the carbon atoms with the substituent is not necessary.

(ex: 1-chlorocyclobutane or cholorocyclobutane is acceptable)

7) If there is more than one of the same functional group on one carbon, write the number of the carbon two, three, or four times,
depending on how many of the same functional group is present on that carbon. The numbers must be separated by commas, and the name
of the functional group that follows must be separated by a dash. When there are two of the same functional group, the name must have the
prefix "di". When there are three of the same functional group, the name must have the prefix "tri". When there are four of the same
functional group, the name must have the prefix "tetra". However, these prefixes cannot be used when determining the alphabetical
priorities.
There must always be commas between the numbers and the dashes that are between the numbers and the names.

EXAMPLE 4.1.2

4.2.3 Updated 7/7/2019

 (2-bromo-1,1-dimethylcyclohexane)

Notice that "f" of fluoro alphabetically precedes the "m" of methyl. Although "di" alphabetically precedes "f", it is not used in determining
the alphabetical order.

EXAMPLE 4.1.3

(2-fluoro-1,1,-dimethylcyclohexane NOT 1,1-dimethyl-2-fluorocyclohexane)

8) If the substituents of the cycloalkane are related by the cis or trans configuration, then indicate the configuration by placing "cis-" or
"trans-" in front of the name of the structure.

Blue=Carbon Yellow=Hydrogen Green=Chlorine

Notice that chlorine and the methyl group are both pointed in the same direction on the axis of the molecule; therefore, they are cis.

cis-1-chloro-2-methylcyclopentane
9) After all the functional groups and substituents have been mentioned with their corresponding numbers, the name of the cycloalkane can
follow.

REACTIVITY
Cycloalkanes are very similar to the alkanes in reactivity, except for the very small ones, especially cyclopropane. Cyclopropane is
significantly more reactive than what is expected because of the bond angles in the ring. Normally, when carbon forms four single bonds,
the bond angles are approximately 109.5°. In cyclopropane, the bond angles are 60°.

With the electron pairs this close together, there is a significant amount of repulsion between the bonding pairs joining the carbon atoms,
making the bonds easier to break.

ALCOHOL SUBSTITUENTS ON CYCLOALKANES

Alcohol (-OH) substituents take the highest priority for carbon atom numbering in IUPAC nomenclature. The carbon atom with the alcohol
substituent must be labeled as 1. Molecules containing an alcohol group have an ending "-ol", indicating the presence of an alcohol group.
If there are two alcohol groups, the molecule will have a "di-" prefix before "-ol" (diol). If there are three alcohol groups, the molecule will
have a "tri-" prefix before "-ol" (triol), etc.

EXAMPLE 4.1.4
The alcohol substituent is given the lowest number even though the two methyl groups are on the same carbon atom and labeling 1 on
that carbon atom would give the lowest possible numbers. Numbering the location of the alcohol substituent is unnecessary because the
ending "-ol" indicates the presence of one alcohol group on carbon atom number 1.

4.2.4 Updated 7/7/2019

 2,2-dimethylcyclohexanol NOT 1,1-dimethyl-cyclohexane-2-ol

EXAMPLE 4.1.5

3-bromo-2-methylcyclopentanol NOT 1-bromo-2-methyl-cyclopentane-2-ol

EXAMPLE 4.1.6

Blue=Carbon Yellow=Hydrogen Red=Oxygen

trans-cyclohexane-1,2-diol

OTHER SUBSTITUENTS ON CYCLOALKANES

There are many other functional groups like alcohol, which are later covered in an organic chemistry course, and they determine the ending
name of a molecule. The naming of these functional groups will be explained in depth later as their chemical properties are explained.
Name Name ending
alkene -ene

alkyne -yne

alcohol -ol

ether -ether

nitrile -nitrile

amine -amine

aldehyde -al

ketone -one

carboxylic acid -oic acid

ester -oate

amide -amide

Although alkynes determine the name ending of a molecule, alkyne as a substituent on a cycloalkane is not possible because alkynes are
planar and would require that the carbon that is part of the ring form 5 bonds, giving the carbon atom a negative charge.

4.2.5 Updated 7/7/2019

However, a cycloalkane with a triple bond-containing substituent is possible if the triple bond is not directly attached to the ring.

EXAMPLE 4.1.7

ethynylcyclooctane

EXAMPLE 4.1.8

1-propylcyclohexane

SUMMARY
1. Determine the parent chain: the parent chain contains the most carbon atoms.
2. Number the substituents of the chain so that the sum of the numbers is the lowest possible.
3. Name the substituents and place them in alphabetical order.
4. If stereochemistry of the compound is shown, indicate the orientation as part of the nomenclature.
5. Cyclic hydrocarbons have the prefix "cyclo-" and have an "-alkane" ending unless there is an alcohol substituent present. When an
alcohol substituent is present, the molecule has an "-ol" ending.

GLOSSARY
alcohol: An oxygen and hydrogenOH hydroxyl group that is bonded to a substituted alkyl group.
alkyl: A structure that is formed when a hydrogen atom is removed from an alkane.
cyclic: Chemical compounds arranged in the form of a ring or a closed chain form.
cycloalkanes: Cyclic saturated hydrocarbons with a general formula of CnH(2n). Cycloalkanes are alkanes with carbon atoms attached
in the form of a closed ring.
functional groups: An atom or groups of atoms that substitute for a hydrogen atom in an organic compound, giving the compound
unique chemical properties and determining its reactivity.
hydrocarbon: A chemical compound containing only carbon and hydrogen atoms.
saturated: All of the atoms that make up a compound are single bonded to the other atoms, with no double or triple bonds.
skeletal structure: A simplified structure in which each intersection between two lines is assumed to have a carbon atom with its
corresponding number of hydrogens.

PROBLEMS
Name the following structures. (Note: The structures are complex for practice purposes and may not be found in nature.)

1) 2) 3) 4) 5) 6)

7)

4.2.6 Updated 7/7/2019

Draw the following structures.
8) 1,1-dibromo-3-butyl-5-fluoro-7-methylcyclooctane 9) trans-1-bromo-2-chlorocyclopentane
10) 1,1-dibromo-2,3-dichloro-4-propylcyclobutane 11) 1-ethyl-2-methyl-1,3-dipropylcyclopentane 12) cycloheptane-1,3,5-triol
Name the following structures.
Blue=Carbon Yellow=Hydrogen Red=Oxygen Green=Chlorine

13) 14) 15) 16) 17)

18) 19)

ANSWERS TO PRACTICE PROBLEMS

1) cyclodecane 2) chlorocyclopentane or 1-chlorocyclopentane 3) trans-1-chloro-2-methylcycloheptane
4) 6-methyl-3-cyclopropyldecane 5) cyclopentylcyclodecane or 1-cyclopentylcyclodecane 6) 1,3-dibromo-1-chloro-2-fluorocycloheptane
7) 1-cyclobutyl-4-isopropylcyclohexane

8) 9) 10) 11) 12)

13) cyclohexane 14) cyclohexanol 15) chlorocyclohexane 16) cyclopentylcyclohexane 17) 1-chloro-3-methylcyclobutane
18) 2,3-dimethylcyclopentanol 19) cis-2-methyl-1-propylcyclopentane

INSIDE LINKS
Nomenclature of Alcohols
Nomenclature of Ethers
Nomenclature of Esters
Nomenclature of Alkenes
Nomenclature of Ketones and Aldehydes
Nomenclature of Alkynes

OUTSIDE LINKS
More Practice Problems on Nomenclature of Cycloalkanes
Vollhardt, Schore. Organic Chemistry. 5th ed.
Wikipedia: Cycloalkanes
http://www.cem.msu.edu/~reusch/VirtualText/nomen1.htm
http://www.chemguide.co.uk/organicprops/alkanes/background.html
http://www.cem.msu.edu/~reusch/VirtualText/nomen1.htm
http://science.csustan.edu/nhuy/chem...IVNamecyal.htm
http://en.wikibooks.org/wiki/Organic...s/Cycloalkanes

REFERENCES
1. ACD/ChemSketch Freeware, version 11.0, Advanced Chemistry Development, Inc., Toronto, ON, Canada, www.acdlabs.com, 2008.
2. Bruice, Paula Yurkanis. Oragnic Chemistry. 5th. CA. Prentice Hall, 2006.
3. Fryhle, C.B. and G. Solomons. Organic Chemistry. 9th ed. Danvers, MA: Wiley, 2008.
4. McMurry, John. Organic Chemistry. 7th ed. Belmont, California: Thomson Higher Education, 2008.
5. Sadava, Heller, Orians, Purves, Hillis. Life The Science of Biology. 8th ed. Sunderland, MA: W.H. Freeman, 2008.
6. Vollhardt, K. Peter C., and Neil E. Schore. Organic Chemistry. 5th ed. New York: W.H. Freeman, 2007.

EXERCISES

4.2.7 Updated 7/7/2019

QUESTIONS
Q4.1.1
Name the following compounds:

Q4.1.2
Draw the following structures
1 = 1,2-dimethylcyclohexane
2 = 2-cyclopropyl butane
3 = 1,2,3-trimethyl cyclopentane
SOLUTIONS
S4.1.1
1 = 1-cyclopropyl cyclopropane
2 = 1-isopropyl cyclohexane
3 = 2-propenyl cyclopentane

CONTRIBUTORS
Pwint Zin
Jim Clark (ChemGuide)
Dr. Dietmar Kennepohl FCIC (Professor of Chemistry, Athabasca University)
Prof. Steven Farmer (Sonoma State University)
Organic Chemistry With a Biological Emphasis by Tim Soderberg (University of Minnesota, Morris)

4.2.8 Updated 7/7/2019

4.3: CIS-TRANS ISOMERISM IN CYCLOALKANES
OBJECTIVES
After completing this section, you should be able to
1. recognize that a formula of the type Cn H2n may represent a cycloalkane.
2. draw structural formulas that distinguish between cis and trans disubstituted cycloalkanes.
3. construct models of cis and trans disubstituted cycloalkanes using ball-and-stick molecular models.

KEY TERMS
Make certain that you can define, and use in context, the key terms below.
cis-trans isomers
cycloalkane
stereoisomer

STUDY NOTES
Compounds in which the carbon atoms are joined in a ring, and in which no multiple bonds or other functional groups are present,
are called cycloalkanes. A cycloalkane containing only one ring will correspond to the general formula CnH2n, but alkenes
containing only one double bond also correspond to this formula. Cycloalkanes containing more than one ring are not considered in
this section.

Stereoisomers are also observed in certain disubstituted (and higher substituted) cyclic compounds. Unlike the relatively flat molecules
of alkenes, substituted cycloalkanes must be viewed as three-dimensional configurations in order to appreciate the spatial orientations
of the substituents. By agreement, chemists use heavy, wedge-shaped bonds to indicate a substituent located above the average plane of
the ring, and a hatched line for bonds to atoms or groups located below the ring. As in the case of the 2-butene stereoisomers,
disubstituted cycloalkane stereoisomers may be designated by nomenclature prefixes such as cis and trans. The stereoisomeric 1,2-
dibromocyclopentanes below are an example.

In general, if any two sp3 carbons in a ring have two different substituent groups (not counting other ring atoms) stereoisomerism is
possible. This is similar to the substitution pattern that gives rise to stereoisomers in alkenes; indeed, one might view a double bond as
a two-membered ring. Four other examples of this kind of stereoisomerism in cyclic compounds are shown below.

4.3.1 Updated 7/7/2019

If more than two ring carbons have different substituents (not counting other ring atoms) the stereochemical notation distinguishing the
various isomers becomes more complex. However, we can always state the relationship of any two substituents using cis or trans. For
example, in the trisubstitutued cyclohexane below, we can say that the methyl group is cis to the ethyl group, and trans to the chlorine.
We can also say that the ethyl group is trans to the chlorine. We cannot, however, designate the entire molecule as a cis or trans isomer.

EXERCISES
QUESTIONS
Q4.2.1
Draw the following molecules:
trans-1,3-dimethylcyclohexane
trans-1,2-dibromocyclopentane
cis-1,3-dichlorocyclobutane
SOLUTIONS
S4.2.1

4.3.2 Updated 7/7/2019

CONTRIBUTORS
Dr. Dietmar Kennepohl FCIC (Professor of Chemistry, Athabasca University)
Prof. Steven Farmer (Sonoma State University)
Organic Chemistry With a Biological Emphasis by Tim Soderberg (University of Minnesota, Morris)

4.3.3 Updated 7/7/2019

4.4: STABILITY OF CYCLOALKANES - RING STRAIN
OBJECTIVES
After completing this section, you should be able to
1. describe the Baeyer strain theory.
2. describe how the measurement of heats of combustion can be used to provide information about the amount of strain present in an alicyclic ring.
3. explain the inadequacies of the Baeyer strain theory.
4. determine which of two similar compounds is likely to be the most stable, by assessing such factors as angle strain, torsional strain and steric strain.

KEY TERMS
Make certain that you can define, and use in context, the key terms below.
angle strain
heat of combustion
steric strain
torsional strain

Cycloalkanes have one or more rings of carbon atoms. The simplest examples of this class consist of a single, unsubstituted carbon ring, and these form a homologous series similar to the unbranched
alkanes. The IUPAC names of the first five members of this series are given in the following table. The last (yellow shaded) column gives the general formula for a cycloalkane of any size. If a simple
unbranched alkane is converted to a cycloalkane two hydrogen atoms, one from each end of the chain, must be lost. Hence the general formula for a cycloalkane composed of n carbons is CnH2n. Although
a cycloalkane has two fewer hydrogens than the equivalent alkane, each carbon is bonded to four other atoms so such compounds are still considered to be saturated with hydrogen.
Table 4.4.1: Examples of Simple Cycloalkanes
Name Cyclopropane Cyclobutane Cyclopentane Cyclohexane Cycloheptane Cycloalkane

Molecular
C3H6 C4H8 C5H10 C6H12 C7H14 CnH2n
Formula

Structural
(CH2)n
Formula

Line
Formula

THE BAEYER THEORY ON THE STRAIN IN CYCLOALKANE RINGS

Many of the properties of cyclopropane and its derivatives are similar to the properties of alkenes. In 1890, the famous German organic chemist, A. Baeyer, suggested that cyclopropane and cyclobutane
derivatives are different from cyclopentane and cyclohexane, because their C—C—C angles cannot have the tetrahedral value of 109.5°. At the same time, Baeyer hypothesized that the difficulties
encountered in synthesizing cycloalkane rings from C7 upward was the result of the angle strain that would be expected if the large rings were regular planar polygons (Table 4.4.1). Baeyer also believed
that cyclohexane had a planar structure like that shown in Figure 12-2, which would mean that the bond angles would have to deviate 10.5° from the tetrahedral value. However, in 1895, the then unknown
chemist H. Sachse suggested that cyclohexane exists in the strain-free chair and boat forms discussed in Section 12-3. This suggestion was not accepted at the time because it led to the prediction of several
possible isomers for compounds such as chlorocyclohexane (cf. Exercise 12-4). The idea that such isomers might act as a single substance, as the result of rapid equilibration, seemed like a needless
complication, and it was not until 1918 that E. Mohr proposed a definitive way to distinguish between the Baeyer and Sachse cyclohexanes. As will be discussed in Section 12-9, the result, now known as
the Sachse-Mohr theory, was complete confirmation of the idea of nonplanar large rings.
Table 4.4.2: Strain in Cycloalkane Rings and Heats of Combustion of Cycloalkanes
Compound n Angle Strain at each CH2 Heat of Combustion ΔHo (kcal/mol) Heat of Combustion ΔHo per CH2/N

ethene 2 109.5 337.2 168.6

cyclopropane 3 49.5 499.9 166.6

cyclobutane 4 19.5 655.9 164.0

cyclopentane 5 1.5 793.4 158.7

cyclohexane 6 10.5 944.8 157.5

cycloheptane 7 19.1 1108.1 158.4

cyclooctane 8 25.5 1268.9 158.6

cyclononane 9 30.5 1429.5 158.8

cyclodecane 10 34.5 1586.1 158.6

cyclopentadecane 15 46.5 2362.5 157.5

open chain alkane 157.4

One of the most interesting developments in ‘the stereochemistry of organic compounds in recent years has been the demonstration that transcyclooctene (but not the cis isomer) can be resolved into stable
chiral isomers (enantiomers, Section 5-IB). In general, a trans-cycloalkene would not be expected to be resolvable because of the possibility for formation of achiral conformations with a plane of
symmetry. Any conformation with all of the carbons in a plane is such an achiral conformation (Figure 12-20a). However, when the chain connecting the ends of the double bond is short, as in trans-
cyclooctene, steric hindrance and steric strain prevent easy.

RING STRAIN IN CYCLOALKANES

Ring Strain occurs because the carbons in cycloalkanes are sp3 hybridized, which means that they do not have the expected ideal bond angle of 109.5o ; this causes an increase in the potential energy
because of the desire for the carbons to be at an ideal 109.5o. An example of ring strain can be seen in the diagram of cyclopropane below in which the bond angle is 60o between the carbons.

4.4.1 Updated 7/7/2019

The reason for ring strain can be seen through the tetrahedral carbon model. The C-C-C bond angles in cyclopropane (diagram above) (60o) and cyclobutane (90o) are much different than the ideal bond
angle of 109.5o. This bond angle causes cyclopropane and cyclobutane to have a high ring strain. However, molecules, such as cyclohexane and cyclopentane, would have a much lower ring strain because
the bond angle between the carbons is much closer to 109.5o.
Below are some examples of cycloalkanes. Ring strain can be seen more prevalently in the cyclopropane and cyclobutane models.

Below is a chart of cycloalkanes and their respective heats of combustion (ΔHcomb). The ΔHcomb value increases as the number of carbons in the cycloalkane increases (higher membered ring), and the
ΔHcomb/CH2 ratio decreases. The increase in ΔHcomb can be attributed to the greater amount of London Dispersion forces. However, the decrease in ΔHcomb/CH2can be attributed to a decrease in the ring
strain.

Certain cycloalkanes, such as cyclohexane, deal with ring strain by forming conformers. A conformer is a stereoisomer in which molecules of the same connectivity and formula exist as different isomers,
in this case, to reduce ring strain. The ring strain is reduced in conformers due to the rotations around the sigma bonds. More about cyclohexane and its conformers can be seen here.
DIFFERENT TYPES OF STRAIN
There are many different types of strain that occur with cycloalkanes. In addition to ring strain, there is also transannular strain, eclipsing, or torsional strain and bond angle strain. Transannular strain exists
when there is steric repulsion between atoms. Eclipsing (torsional) strain exists when a cycloalkane is unable to adopt a staggered conformation around a C-C bond, and bond angle strain is the energy
needed to distort the tetrahedral carbons enough to close the ring. The presence of angle strain in a molecule indicates that there are bond angles in that particular molecule that deviate from the ideal bond
angles required (i.e., that molecule has conformers).

EXERCISES
QUESTIONS
Q4.3.1
trans-1,2-Dimethylcyclobutane is more stable than cis-1,2-dimethylcyclobutane. Explain this observation.
SOLUTIONS
S4.3.1
The trans form does not have eclipsing methyl groups, therefore lowering the energy within the molecule. It does however have hydrogen-methyl interactions, but are not as high in energy than methyl-
methyl interactions.

4.4.2 Updated 7/7/2019

4.5: CONFORMATIONS OF CYCLOALKANES
OBJECTIVES
After completing this section, you should be able to
1. describe, and sketch the conformation of, cyclopropane, cyclobutane and cyclopentane.
2. describe the bonding in cyclopropane, and hence account for the high reactivity of this compound.
3. analyse the stability of cyclobutane, cyclopentane and their substituted derivatives in terms of angular strain, torsional strain and
steric interactions.

STUDY NOTES
Notice that in both cyclobutane and cyclopentane, torsional strain is reduced at the cost of increasing angular (angle) strain.

Although the customary line drawings of simple cycloalkanes are geometrical polygons, the actual shape of these compounds in most
cases is very different.

Cyclopropane is necessarily planar (flat), with the carbon atoms at the corners of an equilateral triangle. The 60º bond angles are much
smaller than the optimum 109.5º angles of a normal tetrahedral carbon atom, and the resulting angle strain dramatically influences the
chemical behavior of this cycloalkane. Cyclopropane also suffers substantial eclipsing strain, since all the carbon-carbon bonds are
fully eclipsed. Cyclobutane reduces some bond-eclipsing strain by folding (the out-of-plane dihedral angle is about 25º), but the total
eclipsing and angle strain remains high. Cyclopentane has very little angle strain (the angles of a pentagon are 108º), but its eclipsing
strain would be large (about 10 kcal/mol) if it remained planar. Consequently, the five-membered ring adopts non-planar puckered
conformations whenever possible.
Rings larger than cyclopentane would have angle strain if they were planar. However, this strain, together with the eclipsing strain
inherent in a planar structure, can be relieved by puckering the ring. Cyclohexane is a good example of a carbocyclic system that
virtually eliminates eclipsing and angle strain by adopting non-planar conformations. Cycloheptane and cyclooctane have greater strain
than cyclohexane, in large part due to transannular crowding (steric hindrance by groups on opposite sides of the ring).
Cyclic systems are a little different from open-chain systems. In an open chain, any bond can be rotated 360 degrees, going through
many different conformations. That complete rotation isn't possible in a cyclic system, because the parts that you would be trying to
twist away from each other would still be connected together. Cyclic systems have fewer "degrees of freedom" than aliphatic systems;
they have "restricted rotation".
Because of the restricted rotation of cyclic systems, most of them have much more well-defined shapes than their aliphatic
counterparts. Let's take a look at the basic shapes of some common rings.
Many biologically important compounds are built around structures containing rings, so it's important that we become familiar with
them.
In nature, three- to six-membered rings are frequently encountered, so we'll focus on those.

CYCLOPROPANE
A three membered ring has no rotational freedom whatsoever. A plane is defined by three points, so the three carbon atoms in
cyclopropane are all constrained to lie in the same plane.

Furthermore, if you look at a model you will find that the neighboring C-H bonds (C-C bonds, too) are all held in eclipsed
conformations.

4.5.1 Updated 7/7/2019

Cyclopropane is always at maximum torsional strain. This strain can be illustrated in a line drawing of cyclopropane as shown from the
side. In this oblique view, the dark lines mean that those sides of the ring are closer to you.

However, the ring isn't big enough to introduce any steric strain, which does not become a factor until we reach six membered rings.
Until that point, rings are not flexible enough for two atoms to reach around and bump into each other.
The really big problem with cyclopropane is that the C-C-C bond angles are all too small.
All the carbon atoms in cyclopropane appear to be tetrahedral.
These bond angles ought to be 109 degrees.
The angles in an equilateral triangle are actually 60 degrees, about half as large as the optimum angle.
This factor introduces a huge amount of strain in the molecule, called ring strain.

CYCLOBUTANE
Cyclobutane is a four membered ring. In two dimensions, it is a square, with 90 degree angles at each corner.

However, in three dimensions, cyclobutane is flexible enough to buckle into a "butterfly" shape, relieving torsional strain a little bit.
When it does that, the bond angles get a little worse, going from 90 degrees to 88 degrees.
In a line drawing, this butterfly shape is usually shown from the side, with the near edges drawn using darker lines.

With bond angles of 88 rather than 109 degrees, cyclobutane has a lot of ring strain, but less than in cyclopropane.
Torsional strain is still present, but the neighbouring bonds are not exactly eclipsed in the butterfly.
Cyclobutane is still not large enough that the molecule can reach around to cause crowding. Steric strain is very low.
Cyclobutanes are a little more stable than cyclopropanes and are also a little more common in nature.

CYCLOPENTANE
Cyclopentanes are even more stable than cyclobutanes, and they are the second-most common paraffinic ring in nature, after
cyclohexanes. In two dimensions, a cyclopentane appears to be a regular pentagon.

In three dimensions, there is enough freedom of rotation to allow a slight twist out of this planar shape. In a line drawing, this three-
dimensional shape is drawn from an oblique view, just like cyclobutane.

The ideal angle in a regular pentagon is about 107 degrees, very close to a tetrahedral bond angle.
Cyclopentane distorts only very slightly into an "envelope" shape in which one corner of the pentagon is lifted up above the plane
of the other four, and as a result, ring strain is entirely removed.
The envelope removes torsional strain along the sides and flap of the envelope. However, the neighbouring carbons are eclipsed
along the "bottom" of the envelope, away from the flap. There is still some torsional strain in cyclopentane.
Again, there is no steric strain in this system.

4.5.2 Updated 7/7/2019

EXERCISES
QUESTIONS
Q4.4.1
If cyclobutane were to be planar how many H-H eclipsing interactions would there be, and assuming 4 kJ/mol per H-H eclipsing
interaction what is the strain on this “planar” molecule?
Q4.4.2
In the two conformations of cis-cyclopentane one is more stable than the other. Explain why this is.

SOLUTIONS
S4.4.1
There are 8 eclipsing interactions (two per C-C bond). The extra strain on this molecule would be 32 kJ/mol (4 kJ/mol x 8).
S4.4.2
The first conformation is more stable. Even though the methyl groups are cis in the model on the left, they are eclipsing due the
conformation, therefore increasing the strain within the molecule.

CONTRIBUTORS
Dr. Dietmar Kennepohl FCIC (Professor of Chemistry, Athabasca University)
Prof. Steven Farmer (Sonoma State University)
Chris P Schaller, Ph.D., (College of Saint Benedict / Saint John's University)
William Reusch, Professor Emeritus (Michigan State U.), Virtual Textbook of Organic Chemistry

4.5.3 Updated 7/7/2019

4.6: CONFORMATIONS OF CYCLOHEXANE
OBJECTIVES
After completing this section, you should be able to
1. explain why cyclohexane rings are free of angular strain.
2. draw the conventional shorthand structure of a cyclohexane ring.

KEY TERMS
Make certain that you can define, and use in context, the key terms below.
chair conformation
twist-boat conformation

Rings larger than cyclopentane would have angle strain if they were planar. However, this strain, together with the eclipsing strain
inherent in a planar structure, can be relieved by puckering the ring. Cyclohexane is a good example of a carbocyclic system that
virtually eliminates eclipsing and angle strain by adopting non-planar conformations. Cycloheptane and cyclooctane have greater strain
than cyclohexane, in large part due to transannular crowding (steric hindrance by groups on opposite sides of the ring).
CONFORMATIONS OF CYCLOHEXANE
A planar structure for cyclohexane is clearly improbable. The bond angles would necessarily be 120º, 10.5º larger than the ideal
tetrahedral angle. Also, every carbon-carbon bond in such a structure would be eclipsed. The resulting angle and eclipsing strains
would severely destabilize this structure. If two carbon atoms on opposite sides of the six-membered ring are lifted out of the plane of
the ring, much of the angle strain can be eliminated.

This boat structure still has two eclipsed bonds and severe steric crowding of two hydrogen atoms on the "bow" and "stern" of the boat.
This steric crowding is often called steric hindrance. By twisting the boat conformation, the steric hindrance can be partially relieved,
but the twist-boat conformer still retains some of the strains that characterize the boat conformer. Finally, by lifting one carbon above
the ring plane and the other below the plane, a relatively strain-free 'chair' conformer is formed. This is the predominant structure
adopted by molecules of cyclohexane.

EXERCISES
QUESTIONS
Q4.5.1
Consider the conformations of cyclohexane, chair, boat, twist boat. Order them in increasing strain in the molecule.
SOLUTIONS
S4.5.1
Chair < Twist Boat < Boat (most strain)

CONTRIBUTORS
Robert Bruner (http://bbruner.org)
William Reusch, Professor Emeritus (Michigan State U.), Virtual Textbook of Organic Chemistry

4.6.1 Updated 7/7/2019

4.7: AXIAL AND EQUATIORIAL BONDS IN CYCLOHEXANE
OBJECTIVES
After completing this section, you should be able to
1. sketch the shorthand structure of cyclohexane, with axial and equatorial hydrogen atoms clearly shown and identified.
2. identify the axial and equatorial hydrogens in a given sketch of the cyclohexane molecule.
3. explain how chair conformations of cyclohexane and its derivatives can interconvert through the process of ring flip.

KEY TERMS
Make certain that you can define, and use in context, the key terms below.
axial position
equatorial position
ring flip

On careful examination of a chair conformation of cyclohexane, we find that the twelve hydrogens are not structurally equivalent. Six
of them are located about the periphery of the carbon ring, and are termed equatorial. The other six are oriented above and below the
approximate plane of the ring (three in each location), and are termed axial because they are aligned parallel to the symmetry axis of
the ring.

In the figure above, the equatorial hydrogens are colored blue, and the axial hydrogens are in bold. Since there are two equivalent chair
conformations of cyclohexane in rapid equilibrium, all twelve hydrogens have 50% equatorial and 50% axial character. The figure
below illustrates how to convert a molecular model of cyclohexane between two different chair conformations - this is something that
you should practice with models. Notice that a 'ring flip' causes equatorial hydrogens to become axial, and vice-versa.

HOW TO DRAW STEREO BONDS ("UP" AND "DOWN" BONDS)

There are various ways to show these orientations. The solid (dark) "up wedge" I used is certainly common. Some people use an
analogous "down wedge", which is light, to indicate a down bond; unfortunately, there is no agreement as to which way the wedge
should point, and you are left relying on the lightness of the wedge to know it is "down". The "down bond" avoids this wedge
ambiguity, and just uses some kind of light line. The down bond I used (e.g., in Figure 5B) is a dashed line; IUPAC encourages a series
of parallel lines, something like A down bond of the type IUPAC prefers. It is a series of parallel lines.. What I did is a variation of what is recommended by
IUPAC: http://www.chem.qmul.ac.uk/iupac/stereo/intro.html.

In ISIS/Draw, the "up wedge" and "down bond" that I used, along with other variations, are
available from a tool button that may be labeled with any of them, depending on most
recent use. It is located directly below the tool button for ordinary C-C bonds.

4.7.1 Updated 7/7/2019

 In Symyx Draw, the "up wedge" and "down bond", along with other variations, are
available from a tool button that may be labeled with any of them, depending on most
recent use. It is located directly below the "Chain" tool button.
ChemSketch provides up and down wedges, but not the simple up and down bonds
discussed above. The wedges are available from the second toolbar across the top. For an
expanded discussion of using these wedges, see the section of my ChemSketch Guide on
Stereochemistry: Wedge bonds.
As always, the information provided on these pages in intended to help you get started.
Each program has more options for drawing bonds than discussed here. When you feel the
need, look around!

HOW TO DRAW CHAIRS

Most of the structures shown on this page were drawn with the free program ISIS/Draw. I have posted a guide to help you get started
with ISIS/Draw. ISIS/Draw provides a simple cyclohexane (6-ring) hexagon template on the toolbar across the top. It provides
templates for various 6-ring chair structures from the Templates menu; choose Rings. There are templates for simple chairs, without
substituents (e.g., Fig 1B), and for chairs showing all the substituents (e.g., Fig 2B). In either case, you can add, delete, or change
things as you wish. Various kinds of stereo bonds (wedges and bars) are available by clicking the left-side tool button that is just below
the regular C-C single bond button. It may have a wedge shown on it, but this will vary depending on how it has been used. To choose
a type of stereo bond, click on the button and hold the mouse click; a new menu will appear to the right of the button.
The free drawing program Symyx Draw, the successor to ISIS/Draw, provides similar templates and tools. A basic chair structure is
provided on the default template bar that is shown. More options are available by choosing the Rings template. See my page Symyx
Draw for a general guide for getting started with this program.
The free drawing program ChemSketch provides similar templates and tools. To find the special templates for chairs, go to the
Templates menu, choose Template Window, and then choose "Rings" from the drop-down menu near upper left. See my page
ChemSketch for a general guide for getting started with this program.
If you want to draw chair structures by hand (and if you are going on in organic chemistry, you should)... Be careful. The precise zigs
and zags, and the angles of substituents are all important. Your textbook may offer you some hints for how to draw chairs. A short item
in the Journal of Chemical Education offers a nice trick, showing how the chair can be thought of as consisting of an M and a W. The
article is V Dragojlovic, A method for drawing the cyclohexane ring and its substituents. J Chem Educ 78:923, 7/01. (I thank M Farooq
Wahab, Chemistry, Univ Karachi, for suggesting that this article be noted here.)
Aside from drawing the basic chair, the key points in adding substituents are:
Axial groups alternate up and down, and are shown "vertical".
Equatorial groups are approximately horizontal, but actually somewhat distorted from that, so that the angle from the axial group is
a bit more than a right angle -- reflecting the common 109 degree bond angle.
As cautioned before, it is usually easier to draw and see what is happening at the four corners of the chair than at the two middle
positions. Try to use the corners as much as possible.
Because axial bonds are parallel to each other, substituents larger than hydrogen generally suffer greater steric crowding when they are
oriented axial rather than equatorial. Consequently, substituted cyclohexanes will preferentially adopt conformations in which the
larger substituents assume equatorial orientation.

When the methyl group in the structure above occupies an axial position it suffers steric crowding by the two axial hydrogens located
on the same side of the ring.

4.7.2 Updated 7/7/2019

The conformation in which the methyl group is equatorial is more stable, and thus the equilibrium lies in this direction

EXERCISES
QUESTIONS
Q4.6.1
Draw two conformations of cyclohexyl amine (C6H11NH2). Indicate axial and equatorial positions.
Q4.6.2
Draw the two isomers of 1,4-dihydroxylcyclohexane, identify which are equatorial and axial.
Q4.6.3
In the following molecule, label which are equatorial and which are axial, then draw the chair flip (showing labels 1,2,3).

SOLUTIONS
S4.6.1

S4.6.2

S4.6.3
Original conformation: 1 = axial, 2 = equatorial, 3 = axial
Flipped chair now looks like this.

4.7.3 Updated 7/7/2019

CONTRIBUTORS
Dr. Dietmar Kennepohl FCIC (Professor of Chemistry, Athabasca University)
Prof. Steven Farmer (Sonoma State University)
Organic Chemistry With a Biological Emphasis by Tim Soderberg (University of Minnesota, Morris)

4.7.4 Updated 7/7/2019

4.8: CONFORMATIONS OF MONOSUBSTITUTED CYCLOHEXANES
OBJECTIVES
After completing this section, you should be able to
1. account for the greater stability of the equatorial conformers of monosubstituted cyclohexanes compared to their axial
counterparts, using the concept of 1,3‑diaxial interaction.
2. compare the gauche interactions in butane with the 1,3‑diaxial interactions in the axial conformer of methylcyclohexane.
3. arrange a given list of substituents in increasing or decreasing order of 1,3‑diaxial interactions.

KEY TERMS
Make certain that you can define, and use in context, the key term below.
1,3‑diaxial interaction

STUDY NOTES
1,3-Diaxial interactions are steric interactions between an axial substituent located on carbon atom 1 of a cyclohexane ring and the
hydrogen atoms (or other substituents) located on carbon atoms 3 and 5.
Be prepared to draw Newman-type projections for cyclohexane derivatives as the one shown for methylcyclohexane. Note that this
is similar to the Newman projections from chapter 3 such as n-butane.

Newman projections of methylcyclohexane and n‑butane

Because axial bonds are parallel to each other, substituents larger than hydrogen generally suffer greater steric crowding when they are
oriented axial rather than equatorial. Consequently, substituted cyclohexanes will preferentially adopt conformations in which the
larger substituents assume equatorial orientation.

When the methyl group in the structure above occupies an axial position it suffers steric crowding by the two axial hydrogens located
on the same side of the ring.

The conformation in which the methyl group is equatorial is more stable, and thus the equilibrium lies in this direction.
The relative steric hindrance experienced by different substituent groups oriented in an axial versus equatorial location on cyclohexane
may be determined by the conformational equilibrium of the compound. The corresponding equilibrium constant is related to the
energy difference between the conformers, and collecting such data allows us to evaluate the relative tendency of substituents to exist
in an equatorial or axial location.A table of these free energy values (sometimes referred to as A values) may be examined by clicking
here.

4.8.1 Updated 7/7/2019

Looking at the energy values in this table, it is clear that the apparent "size" of a substituent (in terms of its preference for equatorial
over axial orientation) is influenced by its width and bond length to cyclohexane, as evidenced by the fact that an axial vinyl group is
less hindered than ethyl, and iodine slightly less than chlorine.
We noted earlier that cycloalkanes having two or more substituents on different ring carbon atoms exist as a pair (sometimes more) of
configurational stereoisomers. Now we must examine the way in which favorable ring conformations influence the properties of the
configurational isomers. Remember, configurational stereoisomers are stable and do not easily interconvert, whereas, conformational
isomers normally interconvert rapidly. In examining possible structures for substituted cyclohexanes, it is useful to follow two
principles:
i. Chair conformations are generally more stable than other possibilities.
ii. Substituents on chair conformers prefer to occupy equatorial positions due to the increased steric hindrance of axial locations.
Table 4.7.1: A Selection of AG° Values for the Change from Axial to Equatorial Orientation of Substituents for Monosubstituted Cyclohexanes
Substituent −ΔG
o
kcal/mol Substituent o
−ΔG kcal/mol

CH −
3
1.7 O N−
2
1.1

CH H −
2 5
1.8 N≡C− 0.2

(CH ) CH−
3 2
2.2 CH O−
3
0.5

(CH ) C−
3 3
≥ 5.0 0.7

F− 0.3 1.3

Cl− 0.5 C H −
6 5
3.0

Br− 0.5

I− 0.5

CHLOROCYCLOHEXANE
This is an example of the next level of complexity, a mono-substituted cycloalkane. See Fig 3.
Chlorocyclohexane: simple hexagon and chair structures, showing hydrogen atoms.

Figure 4.7.3:
So what is new here? Not much, with the hexagon formula, Fig 3A. That type of formula shows the basic "connectivity" of the atoms -
- who is connected to whom. This chemical has one Cl on the ring, and it does not matter where we show it. There is now only one H
on that C, but since we are not showing H explicitly here, that is not an issue in drawing the structure. (It is an issue when you look at it
and want to count H.)
With the chair formula (Fig 3B), which shows information not only about connectivity but also about conformation, there is important
new information here. In a chair, there are two "types" of substituents: those pointing up or down, and called axial, and those pointing
"outward", and called equatorial. I have shown the chlorine atom in an equatorial position. Why? Two reasons: it is what we would
predict, and it is what is found. Why do we predict that the Cl is equatorial? Because it is bigger than H, and there is more room in the
equatorial positions.

HELPFUL HINTS
If possible, examine a physical model of cyclohexane and chlorocyclohexane, so that you can see the axial and equatorial positions.
Common ball and stick models are fine for this. It should be easy to see that the three axial H on one side can get very near each
other.

4.8.2 Updated 7/7/2019

 If you do not have access to physical models, examining computer models can also be useful. When putting substituents on chair
structures, I encourage you to use the four corner positions of the chair as much as possible. It is easier to see the axial and
equatorial relationship at the corners.
In Fig 3B I have shown the H atom that is on the same carbon as the Cl atom. This is perhaps not necessary, since the correct
number of H atoms is understood, by counting bonds on C. But showing the H explicitly at key C atoms helps to make the structure
clearer. This may be particularly important with hand-drawn structures. I often see structures where I am not sure whether a
particular atom is shown axial or equatorial. But if both atoms at the position (the H as well as the Cl) are shown, then hopefully it
becomes clearer which is which. I also encourage students who are not sure of their art work to annotate their drawing. Say what
you mean. That allows me to distinguish whether you are unsure which direction things point or simply unsure how to draw them.)
For notes on how to draw chairs (by hand or using a drawing program), see the section E.2. Note: How to draw chairs.

EXERCISES
QUESTIONS
Q4.7.1
In the molecule, cyclohexyl ethyne there is little steric strain, why?
SOLUTIONS
S4.7.1
The ethyne group is linear and therefore does not affect the hydrogens in the 1,3 positions to say to the extent as a bulkier or a bent
group (e.g. ethene group) would. This leads to less of a strain on the molecule.

CONTRIBUTORS
Dr. Dietmar Kennepohl FCIC (Professor of Chemistry, Athabasca University)
Prof. Steven Farmer (Sonoma State University)
Robert Bruner (http://bbruner.org)
Organic Chemistry With a Biological Emphasis by Tim Soderberg (University of Minnesota, Morris)

4.8.3 Updated 7/7/2019

4.9: CONFORMATIONS OF DISUBSTITUTED CYCLOHEXANES
OBJECTIVE
After completing this section, you should be able to use conformational analysis to determine the most stable conformation of a
given disubstituted cyclohexane.

KEY TERMS
Make certain that you can define, and use in context, the key term below.
conformational analysis

STUDY NOTES
When faced with the problem of trying to decide which of two conformers of a given disubstituted cyclohexane is the more stable,
you may find the following generalizations helpful.
1. A diequatorial conformation will always be more stable than a diaxial one.
2. When one substituent is axial and the other is equatorial, the most stable conformation will be the one with the bulkiest
substituent in the equatorial position. Steric bulk decreases in the order
tert-butyl > isopropyl > ethyl > methyl > hydroxyl > halogens

MONOSUBSTITUTED CYCLOHEXANES
The conformation in which the methyl group is equatorial is more stable, and thus the equilibrium lies in this direction.

The relative steric hindrance experienced by different substituent groups oriented in an axial versus equatorial location on cyclohexane
may be determined by the conformational equilibrium of the compound. The corresponding equilibrium constant is related to the
energy difference between the conformers, and collecting such data allows us to evaluate the relative tendency of substituents to exist
in an equatorial or axial location. Table 4.9.1 show some of these free energy values (sometimes referred to as A values).

4.9.1 Updated 7/7/2019

 Table: 4.9.1: Free Energy Differences for Cyclohexyl Substituents
ΔG º (axial–equatorial)
Substituent Group Substituent Group ΔG º (axial–equatorial)
CH3 1.74 kcal mol-1 F 0.3
C2H5 1.8 Cl 0.6
(CH3)2CH 2.2 Br 0.6
(CH3)3C 4.7 I 0.55
CF3 2.4 OH 0.6 - 1.0
C6H5 2.8 OCH3 0.65
CH2=CH 1.6 OCOCH3 0.75
HC≡C 0.45 OSI(CH3)3 0.7
CN 0.2 SH 1.2
CHO 0.7 NH2 1.3 - 1.7
COCH3 1.2 N(CH3)2 2.0
CO2H 1.4 N3 0.5
CO2 Na 2.0 NO2 1.1
CO2CH3 1.3 Si(CH3)3 2.5
COCl 1.3
These "Conformational Energies" or "A values" are -ΔG° 's for axial/equatorial equilibria of
substituted cyclohexanes. The data in this table are averaged from several different
sources. For a more precise and extensive compilation see: E.L.Eliel and S.H.Wilen,
Stereochemistry of Organic Compounds, 1994.
Looking at the energy values in Table 4.9.1, it is clear that the apparent "size" of a substituent (in terms of its preference for equatorial
over axial orientation) is influenced by its width and bond length to cyclohexane, as evidenced by the fact that an axial vinyl group is
less hindered than ethyl, and iodine slightly less than chlorine.
We noted earlier that cycloalkanes having two or more substituents on different ring carbon atoms exist as a pair (sometimes more) of
configurational stereoisomers. Now we must examine the way in which favorable ring conformations influence the properties of the
configurational isomers. Remember, configurational stereoisomers are stable and do not easily interconvert, whereas, conformational
isomers normally interconvert rapidly. In examining possible structures for substituted cyclohexanes, it is useful to follow two
principles:
i. Chair conformations are generally more stable than other possibilities.
ii. Substituents on chair conformers prefer to occupy equatorial positions due to the increased steric hindrance of axial locations.

DICHLOROCYCLOHEXANES
The next level of complexity are di-substituted cycloalkanes and we will use dichlorocyclohexane as the model system for discussing
these compounds. The first question we must ask is which C the two chlorine substituents are on. For now, I want to discuss 1,3-
dichlorocyclohexane. This introduces another issue: are the two Cl on the same side of the ring, or on opposite sides? We call these
"cis" (same side) and "trans" (opposite sides). We focus on one of these, cis-1,3-dichlorocyclohexane. And for now, we will just look at
hexagon structural formulas, leaving the question of conformation for later. Let's go through this one step at a time.
1,3-DICHLOROCYCLOHEXANE
Our first attempt to draw 1,3-dichlorocyclohexane might look something like Figure 4.9.1

4.9.2 Updated 7/7/2019

 Figure 4.9.1
The structure in Figure 4.8.1 is indeed a dichlorocyclohexane. It is even a 1,3-dichlorocyclohexane. However, this structure provides
no information about the orientation of the two Cl atoms relative to the plane of the ring. To show a specific isomer -- cis or trans -- we
must somehow show how the two Cl atoms are oriented relative to the plane of the ring.

CIS-1,3-DICHLOROCYCLOHEXANE
Figure 4.8.2 shows two common ways to show how the substituents are oriented relative to the plane of the ring. The compound shown
here is cis-1,3-dichlorocyclohexane.

Figure 4.9.2
The basic idea in both of these is that we can imagine the ring to be planar, and then show the groups above or below the plane of the
ring. How we show this is different in the two parts of Figure 4.9.2. In Figure 4.9.1A, we look at the ring "edge-on". The thick line for
the bottom bond is intended to convey the edge-on view (or side view); this is sometimes omitted, especially with hand-drawn
structures, but be careful then that the meaning is clear. Once we understand that we are now looking at the ring edge-on, it is clear that
the two Cl atoms are both above the ring, hence cis. In Figure 4.9.2B, we view the ring "face-on" (or top view), and use special bond
symbols -- "stereo bonds" -- to convey up and down: the heavy wedge -- an "up wedge" -- points upward, toward you, and the dashed
bond -- a "down bond" -- points downward, away from you. Again, both Cl are "up", hence cis.

NOTE
For some notes on how to draw the stereo bonds, see the section E.1. Note: How to draw stereo bonds ("up" and "down" bonds).
In discussing Figure 4.9.2, I started by saying that we imagine the ring to be planar. Emphasize that cycloalkane rings are not really
planar (except for cyclopropane rings). As so often, the structural formula represents the general layout of the atoms, but not the
actual molecular geometry.

THE CONFORMATION OF CIS-1,3-DICHLOROCYCLOHEXANE

Figure 4.9.3, at the right, is one way to show this. Figure 4.8.3 shows features of the compound that we have already noted -- plus one
more. Let's go through these features, emphasizing what is new.

Figure 4.9.3
The structure shows cis-1,3-dichlorocyclohexane: a 6-ring; 2 Cl atoms, at positions 1 and 3; and cis, with both Cl on the same side of --
above -- the H that is on the same C.
I showed the 2 Cl atoms at corner positions, and I showed the H at the key positions explicitly. These points follow from some of the
Helpful Hints discussed earlier. It is not required that you do these things, but they can make things easier for you -- and for anyone
reading your structures.
Now, what is new here? The conformation. We start with the notion that the conformation of cyclohexane derivatives is based on the
"chair". At each position, one substituent is axial (loosely, perpendicular to the ring), and one is equatorial (loosely, in the plane of the
ring). There is more room in the equatorial positions (not easily seen with these simple drawings, but ordinary ball and stick models do
help with this point). Thus we try to put the larger substituents in the equatorial positions. In this case, we put the Cl equatorial and the
H axial at each position 1 and position 3.
We are now done with this compound, cis-1,3-dichlorocyclohexane. However, we have missed one very important concern -- because
it is not an issue in this case. So let's look at another compound.

4.9.3 Updated 7/7/2019

CIS-1,2-DICHLOROCYCLOHEXANE
cis-1,2-Dichlorocyclohexane is like the previous compound, except that the two chloro groups are now at 1,2, rather than at 1,3. Figure
4.8.4 shows a simple structural formula for 1,2-dichlorocyclohexane, without orientation. This is analogous to Figure 4.9.1 for the 1,3
isomer.

Figure 4.9.4: 1,2-dichlorocyclohexane: simple hexagon, with no info about orientation.

Figure 4.8.5 shows two ways to show the cis orientation in cis-1,2-dichlorocyclohexane. This Figure is analogous to Figure 4.8.3 above
for the 1,3 isomer.

Figure 4.9.15
Figures 4.9.4 and 4.9.5 introduce no new ideas or complications; these two figures should be straightforward. So, what is the preferred
conformation of cis-1,2-dichlorocyclohexane? This requires careful consideration; an important lesson from this exercise is to realize
that we cannot propose a good conformation based simply on what we have learned so far. The two guidelines we have so far for
conformation of 6-rings are:
The carbon ring is in a chair.
Larger substituents are in equatorial positions.
Let's explore the difficulty here by looking at some things people might naively draw. Figure 4.9.6 shows an attempt to draw a chair
conformation of cis-1,2-dichlorocyclohexane. It satisfies both of the guidelines listed above. But it is wrong.

Figure 4.9.6: An attempt to draw a chair conformation of cis-1,2-dichlorocyclohexane. But this is the wrong chemical.
Why is Figure 4.9.6 wrong? It is the wrong chemical. The structure shown in Figure 4.9.6 is trans, not cis. Look carefully at the 1 and
2 positions. At one of them, the H is above the Cl; at the other, the Cl is above the H. Trans. Wrong chemical. The structure shown in
Figure 4.9.6 is not the requested chemical. Figure 4.9.7 attempts to fix the problem with Figure 4.9.6. However, it is also wrong.

Figure 4.9.7
Why is Figure 4.9.8 wrong? After all, it seems to address the criteria presented. It contains both of the larger atoms (Cl) equatorial, and
they are cis as desired. However, in Figure 4.8.7, the two axial groups on carbons # 1 and 2 (the two H that are shown) are both
pointing up. This is impossible. In a valid chair, the axial groups alternate up/down as one goes around the ring

Figure 4.9.8

4.9.4 Updated 7/7/2019

This follows from the tetrahedral bonding of C. Adjacent axial groups, as relevant here, must point in opposite directions; that
condition is violated here. That is, Figure 4.9.7 is not a valid chair.
So now what? We have a contradiction. And that really is the most important point here. It is important to realize that we cannot draw a
conformation for cis-1,2-dichlorocyclohexane which easily fits the criteria we have used so far: a chair, with large groups equatorial.
So what do we do? Clearly, the conformation of this compound must, in some way, involve more issues than what we have considered
so far.
Instructors and books will vary in how much further explanation they want to give on this matter. Therefore, how you proceed from
here must take into account the preferences in your course. Here is one way to proceed.
One simple way to proceed is to re-examine the two criteria we have been using, and then state a generality about what to do in the
event of a conflict. That generality is: use the chair, and then fit the groups as best you can. That is, try to put as many of the larger
groups equatorial as you can, but realize that you may not get them all equatorial.

Figure 4.9.9: A plausible chair conformation of cis-1,2-dichlorocyclohexane.

What have we accomplished here?
First, this is the correct compound. Convince yourself that this really is cis-1,2-dichlorocyclohexane. In particular, it is cis because
at each substituted position the Cl is "above" the H; that is, both Cl are on the same side of the ring.
Second, this is a proper chair. Adjacent axial groups point in opposite directions. Only two of them are shown here: the axial Cl on
the upper right C is "up", and the axial H on the lower right C is "down". Thus, these aspects satisfy the proper way to orient things,
in general, on a cyclohexane chair.
How good a conformation is the one shown in Figure 4.9.9? Actually, it is quite good, in this case. The actual conformation has been
measured, and it follows the basic ideas shown here.
Is this the end of the story? No, but it is about enough for now. The main purpose here was to show how one must carefully look at
conformation, within the constraints of the specific isomer one is trying to draw. Some compounds cannot be easily drawn within the
common "rules". cis-1,2-dichlorocyclohexane is one such example. In this case, we kept the basic chair conformation, but put one
larger group in the less favored axial orientation. Measurements on many such chemicals have shown that the energetic penalty of
moving a cyclohexane ring much away from the basic chair conformation is quite large -- certainly larger than the energetic penalty of
putting one "somewhat large" group in an axial position. Of course, with larger groups or more groups, this might not hold.

EXERCISES
QUESTIONS
Q4.8.1
For the following molecules draw the most stable chair conformation and explain why you chose this as an answer
1 = trans-1,2-dimethylcyclohexane
2 = cis-1,3-dimethylcyclohexane
SOLUTIONS
S4.8.1
1 – The most stable conformation would be to have the methyl groups axial reducing steric interaction
2 – The most stable conformation would be to have the groups equatorial this would reduce the strain if they were axial

4.9.5 Updated 7/7/2019

CONTRIBUTORS
Dr. Dietmar Kennepohl FCIC (Professor of Chemistry, Athabasca University)
Prof. Steven Farmer (Sonoma State University)
Organic Chemistry With a Biological Emphasis by Tim Soderberg (University of Minnesota, Morris)
Jim Clark (Chemguide.co.uk)
Robert Bruner (http://bbruner.org)

4.9.6 Updated 7/7/2019

4.10: CONFORMATIONS OF POLYCYCLIC MOLECULES
OBJECTIVE
After completing this section, you should be able to draw the structures and construct molecular models of cis- and trans-decalin
and of norbornane.

KEY TERMS
Make certain that you can define, and use in context, the key terms below.
bridgehead carbon atom
polycyclic molecule

STUDY NOTES
A bridgehead carbon atom is a carbon atom which is shared by at least two rings. The hydrogen atom which is attached to a
bridgehead carbon may be referred to as a bridgehead hydrogen.
Note that bicyclo[2.2.1]heptane is the systematic name of norborane. You need not be concerned over the IUPAC name of
norbornane. The nomenclature of compounds of this type is beyond the scope of this course.

BICYCLIC RING SYSTEMS

A bridged bicycloalkane is a bicycloalkane whose molecule has two carbon atoms shared by all three rings identifiable in the molecule.
The two carbon atoms shared by the three rings are called bridgehead carbon atoms. A bond or a chain of bonds connecting the
bridgehead carbon atoms is called a bridge.
eg. 1: Decalin

eg. 2: bicyclo[2.2.1]heptane

4.10.1 Updated 7/7/2019

If in a bridged bicycloalkane, the bridgehead carbons are directly bonded to each other, the compound is called a fused bicycloalkane.
In other words, in a fused bicycloalkane, the number of carbon atoms in one of the three bridges is zero. eg: decalin
see also spirobicycloalkane
Decalins can come in two diastereomers, the trans- or cis- diastereomer. The trans-diastereomer is a rigid structure which cannot
undergo a ring flip. The cis-diastereomer is mobile and can ring flip to allow substituents to sit in the equatorial position.

STEROIDS
Steroids include such well known compounds as cholesterol, sex hormones, birth control pills, cortisone, and anabolic steroids.

CHOLESTEROL
The best known and most abundant steroid in the body is cholesterol. Cholesterol is formed in brain tissue, nerve tissue, and the blood
stream. It is the major compound found in gallstones and bile salts. Cholesterol also contributes to the formation of deposits on the
inner walls of blood vessels. These deposits harden and obstruct the flow of blood. This condition, known as atherosclerosis, results in
various heart diseases, strokes, and high blood pressure.
Much research is currently underway to determine if a correlation exists between cholesterol levels in the blood and diet. Not only does
cholesterol come from the diet, but cholesterol is synthesized in the body from carbohydrates and proteins as well as fat. Therefore, the
elimination of cholesterol rich foods from the diet does not necessarily lower blood cholesterol levels. Some studies have found that if
certain unsaturated fats and oils are substituted for saturated fats, the blood cholesterol level decreases. The research is incomplete on
this problem.

4.10.2 Updated 7/7/2019

STRUCTURES OF SEX HORMONES
Sex hormones are also steroids. The primary male hormone, testosterone, is responsible for the development of secondary sex
characteristics. Two female sex hormones, progesterone and estrogen or estradiol control the ovulation cycle. Notice that the male and
female hormones have only slight differences in structures, but yet have very different physiological effects.
Testosterone promotes the normal development of male genital organs ans is synthesized from cholesterol in the testes. It also
promotes secondary male sexual characteristics such as deep voice, facial and body hair.
Estrogen, along with progesterone regulates changes occurring in the uterus and ovaries known as the menstrual cycle. For more
details see Birth Control. Estrogen is synthesized from testosterone by making the first ring aromatic which results in mole double
bonds, the loss of a methyl group and formation of an alcohol group.

EXERCISES
QUESTIONS
Q4.9.1
Someone stated that trans-decalin is more stable than cis-decalin. Explain why this is incorrect.
SOLUTIONS
S4.9.1
Cis-decalin has fewer steric interactions than trans-decalin.

CONTRIBUTORS
Gamini Gunawardena from the OChemPal site (Utah Valley University)
John D. Robert and Marjorie C. Caserio (1977) Basic Principles of Organic Chemistry, second edition. W. A. Benjamin, Inc. ,
Menlo Park, CA. ISBN 0-8053-8329-8. This content is copyrighted under the following conditions, "You are granted permission
for individual, educational, research and non-commercial reproduction, distribution, display and performance of this work in any
format."

4.10.3 Updated 7/7/2019

5: STEREOCHEMISTRY AT TETRAHEDRAL CENTRES
5.1: CHAPTER OBJECTIVES
5.2: ENANTIOMERS AND THE TETRAHEDRAL CARBON
5.3: THE REASON FOR HANDEDNESS IN MOLECULES - CHIRALITY
5.4: OPTICAL ACTIVITY
5.5: PASTEUR'S DISCOVERY OF ENANTIOMERS
5.6: SEQUENCE RULES FOR SPECIFYING CONFIGURATION
5.7: DIASTEREOMERS
5.8: MESO COMPOUNDS
5.9: RACEMIC MIXTURES AND THE RESOLUTION OF ENANTIOMERS
5.10: A REVIEW OF ISOMERISM
5.11: CHIRALITY AT NITROGEN, PHOSPHORUS, AND SULFUR
5.12: PROCHIRALITY
When a tetrahedral carbon can be converted to a chiral center by changing only one of its attached groups, it is referred to as a
‘prochiral' center.

5.13: CHIRALITY IN NATURE AND CHIRAL ENVIRONMENTS

5.14: 5:3 ENANTIOMERS
5.15: MESO COMPOUNDS

TOC.1 Updated 7/14/2019

5.1: CHAPTER OBJECTIVES
After you have completed Chapter 5, you should be able to
1. fulfill all of the detailed objectives listed under each individual section.
2. use molecular models in solving problems on stereochemistry.
3. solve road-map problems that include stereochemical information.
4. define, and use in context, the new key terms.

CONTRIBUTORS
Dr. Dietmar Kennepohl FCIC (Professor of Chemistry, Athabasca University)

5.1.1 Updated 7/7/2019

5.2: ENANTIOMERS AND THE TETRAHEDRAL CARBON
OBJECTIVES
After completing this section, you should be able to
1. use molecular models to show that only a tetrahedral carbon atom satisfactorily accounts for the lack of isomerism in molecules
of the type CH2XY, and for the existence of optical isomerism in molecules of the type CHXYZ.
2. determine whether two differently oriented wedge-and-broken-line structures are identical or represent a pair of enantiomers.

KEY TERMS
Make certain that you can define, and use in context, the key term below.
enantiomer

STUDY NOTES
Stereoisomers are isomers that differ in spatial arrangement of atoms, rather than order of atomic connectivity. One of their most
interesting type of isomer is the mirror-image stereoisomers, a non-superimposable set of two molecules that are mirror image of
one another. The existance of these molecules are determined by concept known as chirality. The word “chiral” was derived from
the Greek word for hand, because our hands display a good example of chirality since they are non-superimposable mirror images
of each other.

INTRODUCTION
The opposite of chiral is achiral. Achiral objects are superimposable with their mirror images. For example, two pieces of paper are
achiral. In contrast, chiral molecules, like our hands, are non superimposable mirror images of each other. Try to line up your left hand
perfectly with your right hand, so that the palms are both facing in the same directions. Spend about a minute doing this. Do you see
that they cannot line up exactly? The same thing applies to some molecules

A Chiral molecule has a mirror image that cannot line up with it perfectly- the mirror images are non superimposable. The mirror
images are called enantiomers. But why are chiral molecules so interesting? A chiral molecule and its enantiomer have the same
chemical and physical properties(boiling point, melting point,polarity, density etc...). It turns out that many of our biological molecules
such as our DNA, amino acids and sugars, are chiral molecules.
It is pretty interesting that our hands seem to serve the same purpose but most people are only able to use one of their hands to write.
Similarily this is true with chiral biological molecules and interactions. Just like your left hand will not fit properly in your right glove,
one of the enantiomers of a molecule may not work the same way in your body.
This must mean that enantiomers have properties that make them unique to their mirror images. One of these properties is that they
cannot have a plane of symmetry or an internal mirror plane. So, a chiral molecule cannot be divided in two mirror image halves.
Another property of chiral molecules is optical activity.
Organic compounds, molecules created around a chain of carbon atom (more commonly known as carbon backbone), play an essential
role in the chemistry of life. These molecules derive their importance from the energy they carry, mainly in a form of potential energy
between atomic molecules. Since such potential force can be widely affected due to changes in atomic placement, it is important to
understand the concept of an isomer, a molecule sharing same atomic make up as another but differing in structural arrangements. This
article will be devoted to a specific isomers called stereoisomers and its property of chirality (Figure 5.1.1).

5.2.1 Updated 7/7/2019

 Figure 5.1.1. Two enantiomers of a tetrahedral complex. Image used with permission from Wikipedia
The concepts of steroisomerism and chirality command great deal of importance in modern organic chemistry, as these ideas helps to
understand the physical and theoretical reasons behind the formation and structures of numerous organic molecules, the main reason
behind the energy embedded in these essential chemicals. In contrast to more well-known constitutional isomerism, which develops
isotopic compounds simply by different atomic connectivity, stereoisomerism generally maintains equal atomic connections and orders
of building blocks as well as having same numbers of atoms and types of elements.
What, then, makes stereoisomers so unique? To answer this question, the learner must be able to think and imagine in not just two-
dimensional images, but also three-dimensional space. This is due to the fact that stereoisomers are isomers because their atoms are
different from others in terms of spatial arrangement.

SPATIAL ARRANGEMENT
First and foremost, one must understand the concept of spatial arrangement in order to understand stereoisomerism and chirality.
Spatial arrangement of atoms concern how different atomic particles and molecules are situated about in the space around the organic
compound, namely its carbon chain. In this sense, spatial arrangement of an organic molecule are different another if an atom is shifted
in any three-dimensional direction by even one degree. This opens up a very broad possibility of different molecules, each with their
unique placement of atoms in three-dimensional space .

STEREOISOMERS
Stereoisomers are, as mentioned above, contain different types of isomers within itself, each with distinct characteristics that further
separate each other as different chemical entities having different properties. Type called entaniomer are the previously-mentioned
mirror-image stereoisomers, and will be explained in detail in this article. Another type, diastereomer, has different properties and will
be introduced afterwards.

ENANTIOMERS
This type of stereoisomer is the essential mirror-image, non-superimposable type of stereoisomer introduced in the beginning of the
article. Figure 3 provides a perfect example; note that the gray plane in the middle demotes the mirror plane.

Figure 5.1.2.
Note that even if one were to flip over the left molecule over to the right, the atomic spatial arrangement will not be equal. This is
equivalent to the left hand - right hand relationship, and is aptly referred to as 'handedness' in molecules. This can be somewhat
counter-intuitive, so this article recommends the reader try the 'hand' example. Place both palm facing up, and hands next to each other.
Now flip either side over to the other. One hand should be showing the back of the hand, while the other one is showing the palm. They
are not same and non-superimposable. This is where the concept of chirality comes in as one of the most essential and defining idea of
stereoisomerism.
CHIRALITY

5.2.2 Updated 7/7/2019

Chirality essentially means 'mirror-image, non-superimposable molecules', and to say that a molecule is chiral is to say that its mirror
image (it must have one) is not the same as it self. Whether a molecule is chiral or achiral depends upon a certain set of overlapping
conditions. Figure 5.1.1 shows an example of two molecules, chiral and achiral, respectively. Notice the distinct characteristic of the
achiral molecule: it possesses two atoms of same element. In theory and reality, if one were to create a plane that runs through the other
two atoms, they will be able to create what is known as bisecting plane: The images on either side of the plan is the same as the other
(Figure 5.1.3).

Figure 5.1.3.
In this case, the molecule is considered 'achiral'. In other words, to distinguish chiral molecule from an achiral molecule, one must
search for the existence of the bisecting plane in a molecule. All chiral molecules are deprive of bisecting plane, whether simple or
complex. As a universal rule, no molecule with different surrounding atoms are achiral. Chirality is a simple but essential idea to
support the concept of stereoisomerism, being used to explain one type of its kind. The chemical properties of the chiral molecule
differs from its mirror image, and in this lies the significance of chilarity in relation to modern organic chemistry.

CONTRIBUTORS
Dr. Dietmar Kennepohl FCIC (Professor of Chemistry, Athabasca University)
Prof. Steven Farmer (Sonoma State University)
William Reusch, Professor Emeritus (Michigan State U.), Virtual Textbook of Organic Chemistry
Organic Chemistry With a Biological Emphasis by Tim Soderberg (University of Minnesota, Morris)
Jim Clark (Chemguide.co.uk)

5.2.3 Updated 7/7/2019

5.3: THE REASON FOR HANDEDNESS IN MOLECULES - CHIRALITY
OBJECTIVES
After completing this section, you should be able to
1. determine whether or not a compound is chiral, given its Kelulé, condensed or shorthand structure, with or without the aid of
molecular models.
2. label the chiral centres (carbon atoms) in a given Kelulé, condensed or shorthand structure.

KEY TERMS
Make certain that you can define, and use in context, the key terms below.
achiral
chiral
chiral (stereogenic) centre
plane of symmetry

A consideration of the chirality of molecular configurations explains the curious stereoisomerism observed for lactic acid, carvone and
a multitude of other organic compounds. Tetravalent carbons have a tetrahedral configuration. If all four substituent groups are the
same, as in methane or tetrachloromethane, the configuration is that of a highly symmetric "regular tetrahedron". A regular tetrahedron
several planes of symmetry and is achiral.
A carbon atom that is bonded to four different atoms or groups loses all symmetry, and is often referred to as an asymmetric carbon.
The configuration of such a molecular unit is chiral, and the structure may exist in either a right-handed configuration or a left-handed
configuration (one the mirror image of the other). This type of configurational stereoisomerism is termed enantiomorphism, and the
non-identical, mirror-image pair of stereoisomers that result are called enantiomers. In the general figure below, A and B are
nonsuperposable mirror images of one another, and thus are a pair of enantiomers.

The structural formulas of lactic acid and carvone are drawn on the right with the asymmetric carbon colored red. Consequently, we
find that these compounds exist as pairs of enantiomers. The presence of a single asymmetrically substituted carbon atom in a molecule
is sufficient to render the whole configuration chiral, and modern terminology refers to such groupings as chiral centers. Most of the
chiral centers we shall discuss are asymmetric carbon atoms, but it should be recognized that other tetrahedral or pyramidal atoms may
become chiral centers if appropriately substituted. When more than one chiral center is present in a molecular structure, care must be
taken to analyze their relationship before concluding that a specific molecular configuration is chiral or achiral. This aspect of
stereoisomerism will be treated later.

A useful first step in examining structural formulas to determine whether stereoisomers may exist is to identify all stereogenic
elements. A stereogenic element is a center, axis or plane that is a focus of stereoisomerism, such that an interchange of two groups
attached to this feature leads to a stereoisomer. Stereogenic elements may be chiral or achiral. An asymmetric carbon is often a chiral
stereogenic center, since interchanging any two substituent groups converts one enantiomer to the other. Alkenes having two different
groups on each double bond carbon constitute an achiral stereogenic element, since interchanging substituents at one of the carbons
changes the cis/trans configuration of the double bond.

5.3.1 Updated 7/7/2019

Some of the structures in the figure above are chiral and some are achiral. First, try to identify all chiral stereogenic centers. Formulas
having no chiral centers are necessarily achiral. Formulas having one chiral center are always chiral; and if two or more chiral centers
are present in a given structure it is likely to be chiral, but in special cases, to be discussed later, may be achiral.
Structures F and G are achiral. The former has a plane of symmetry passing through the chlorine atom and bisecting the opposite
carbon-carbon bond. The similar structure of compound E does not have such a symmetry plane, and the carbon bonded to the chlorine
is a chiral center (the two ring segments connecting this carbon are not identical). Structure G is essentially flat. All the carbons except
that of the methyl group are sp2 hybridized, and therefore trigonal-planar in configuration. Compounds C, D & H have more than one
chiral center, and are also chiral. Remember, all chiral structures may exist as a pair of enantiomers. Other configurational
stereoisomers are possible if more than one stereogenic center is present in a structure.
In the 1960’s, a drug called thalidomide was widely prescribed in the Western Europe to alleviate morning sickness in pregnant
women.

Thalidomide had previously been used in other countries as an antidepressant, and was believed to be safe and effective for both
purposes. The drug was not approved for use in the U.S.A. It was not long, however, before doctors realized that something had gone
horribly wrong: many babies born to women who had taken thalidomide during pregnancy suffered from severe birth defects.
Researchers later realized the that problem lay in the fact that thalidomide was being provided as a mixture of two different isomeric
forms.

One of the isomers is an effective medication, the other caused the side effects. Both isomeric forms have the same molecular formula
and the same atom-to-atom connectivity, so they are not constitutional isomers. Where they differ is in the arrangement in three-
dimensional space about one tetrahedral, sp3-hybridized carbon. These two forms of thalidomide are stereoisomers.
Note that the carbon in question has four different substituents (two of these just happen to be connected by a ring structure).
Tetrahedral carbons with four different substituent groups are called stereocenters.

EXAMPLE 5.2.1
Locate all of the carbon stereocenters in the molecules below.

5.3.2 Updated 7/7/2019

 Answer:

Looking at the structures of what we are referring to as the two isomers of thalidomide, you may not be entirely convinced that they are
actually two different molecules. In order to convince ourselves that they are indeed different, let’s create a generalized picture of a
tetrahedral carbon stereocenter, with the four substituents designated R1-R4. The two stereoisomers of our simplified model look like
this:

If you look carefully at the figure above, you will notice that molecule A and molecule B are mirror images of each other (the line
labeled 's' represents a mirror plane). Furthermore, they are not superimposable: if we pick up molecule A, flip it around, and place it
next to molecule B, we see that the two structures cannot be superimposed on each other. They are different molecules!

If you make models of the two stereoisomers of thalidomide and do the same thing, you will see that they too are mirror images, and
cannot be superimposed (it well help to look at a color version of the figure below).

5.3.3 Updated 7/7/2019

Thalidomide is a chiral molecule. Something is considered to be chiral if it cannot be superimposed on its own mirror image – in other
words, if it is asymmetric (lacking in symmetry). The term ‘chiral’ is derived from the Greek word for ‘handedness’ – ie. right-
handedness or left-handedness. Your hands are chiral: your right hand is a mirror image of your left hand, but if you place one hand on
top of the other, both palms down, you see that they are not superimposable.
A pair of stereoisomers that are non-superimposable mirror images of one another are considered to have a specific type of
stereoisomeric relationship – they are a pair of enantiomers. Thalidomide exists as a pair of enantiomers. On the macro level, your left
and right hands are also a pair of enantiomers.
Here are some more examples of chiral molecules that exist as pairs of enantiomers. In each of these examples, there is a single
stereocenter, indicated with an arrow. (Many molecules have more than one stereocenter, but we will get to that that a little later!)

Here are some examples of molecules that are achiral (not chiral). Notice that none of these molecules has a stereocenter.

It is difficult to illustrate on the two dimensional page, but you will see if you build models of these achiral molecules that, in each
case, there is at least one plane of symmetry, where one side of the plane is the mirror image of the other. Chirality is tied
conceptually to the idea of asymmetry, and any molecule that has a plane of symmetry cannot be chiral. When looking for a plane of
symmetry, however, we must consider all possible conformations that a molecule could adopt. Even a very simple molecule like
ethane, for example, is asymmetric in many of its countless potential conformations – but it has obvious symmetry in both the eclipsed
and staggered conformations, and for this reason it is achiral.

5.3.4 Updated 7/7/2019

Looking for planes of symmetry in a molecule is useful, but often difficult in practice. In most cases, the easiest way to decide whether
a molecule is chiral or achiral is to look for one or more stereocenters - with a few rare exceptions (see section 3.7B), the general rule is
that molecules with at least one stereocenter are chiral, and molecules with no stereocenters are achiral. Carbon stereocenters are also
referred to quite frequently as chiral carbons.
When evaluating a molecule for chirality, it is important to recognize that the question of whether or not the dashed/solid wedge
drawing convention is used is irrelevant. Chiral molecules are sometimes drawn without using wedges (although obviously this means
that stereochemical information is being omitted). Conversely, wedges may be used on carbons that are not stereocenters – look, for
example, at the drawings of glycine and citrate in the figure above. Just because you see dashed and solid wedges in a structure, do not
automatically assume that you are looking at a stereocenter.
Other elements in addition to carbon can be stereocenters. The phosphorus center of phosphate ion and organic phosphate esters, for
example, is tetrahedral, and thus is potentially a stereocenter.

We will see in chapter 10 how researchers, in order to investigate the stereochemistry of reactions at the phosphate center, incorporated
sulfur and/or 17O and 18O isotopes of oxygen (the ‘normal’ isotope is 16O) to create chiral phosphate groups. Phosphate triesters are
chiral if the three substituent groups are different.
Asymmetric quaternary ammonium groups are also chiral. Amines, however, are not chiral, because they rapidly invert, or turn ‘inside
out’, at room temperature.

EXAMPLE 5.2.2
Label the molecules below as chiral or achiral, and locate all stereocenters.

Answer:

5.3.5 Updated 7/7/2019

EXERCISES
QUESTIONS
Q5.2.1
Identify the chiral centers in each of the following:

SOLUTIONS
S5.2.1

CONTRIBUTORS
Dr. Dietmar Kennepohl FCIC (Professor of Chemistry, Athabasca University)
Prof. Steven Farmer (Sonoma State University)
William Reusch, Professor Emeritus (Michigan State U.), Virtual Textbook of Organic Chemistry
Organic Chemistry With a Biological Emphasis by Tim Soderberg (University of Minnesota, Morris)
Jim Clark (Chemguide.co.uk)

5.3.6 Updated 7/7/2019

5.4: OPTICAL ACTIVITY
OBJECTIVES
After completing this section, you should be able to
1. describe the nature of plane-polarized light.
2. describe the features and operation of a simple polarimeter.
3. calculate the specific rotation of a compound, given the relevant experimental data.

KEY TERMS
Make certain that you can define, and use in context, the key terms below.
analyzer
dextrorotatory
levorotatory
optically active
plane-polarized light
polarimeter
polarizer
specific rotation, [α]D

STUDY NOTES
A polarizer is a device through which only light waves oscillating in a single plane may pass. A polarimeter is an instrument used
to determine the angle through which plane-polarized light has been rotated by a given sample. You will have the opportunity to use
a polarimeter in the laboratory component of the course. An analyzer is the component of a polarimeter that allows the angle of
rotation of plane-polarized light to be determined.
20
Specific rotations are normally measured at 20°C, and this property may be indicated by the symbol [α]D . Sometimes the solvent
is specified in parentheses behind the specific rotation value, for example,
20
[α]
D
= + 12 ° (chloroform)
For liquids, the specific rotation may be obtained using the neat liquid rather than a solution; in such cases the formula is

temp
α
[α] (neat) =
D
l × d

where α is the observed rotation, l is the path length of the cell (measured in decimetres, dm), and d is the density of the liquid.

Identifying and distinguishing enantiomers is inherently difficult, since their physical and chemical properties are largely identical.
Fortunately, a nearly two hundred year old discovery by the French physicist Jean-Baptiste Biot has made this task much easier. This
discovery disclosed that the right- and left-handed enantiomers of a chiral compound perturb plane-polarized light in opposite ways.
This perturbation is unique to chiral molecules, and has been termed optical activity.

POLARIMETRY
Plane-polarized light is created by passing ordinary light through a polarizing device, which may be as simple as a lens taken from
polarizing sun-glasses. Such devices transmit selectively only that component of a light beam having electrical and magnetic field
vectors oscillating in a single plane. The plane of polarization can be determined by an instrument called a polarimeter, shown in the
diagram below.

5.4.1 Updated 7/7/2019

Monochromatic (single wavelength) light, is polarized by a fixed polarizer next to the light source. A sample cell holder is located in
line with the light beam, followed by a movable polarizer (the analyzer) and an eyepiece through which the light intensity can be
observed. In modern instruments an electronic light detector takes the place of the human eye. In the absence of a sample, the light
intensity at the detector is at a maximum when the second (movable) polarizer is set parallel to the first polarizer (α = 0º). If the
analyzer is turned 90º to the plane of initial polarization, all the light will be blocked from reaching the detector.
Chemists use polarimeters to investigate the influence of compounds (in the sample cell) on plane polarized light. Samples composed
only of achiral molecules (e.g. water or hexane), have no effect on the polarized light beam. However, if a single enantiomer is
examined (all sample molecules being right-handed, or all being left-handed), the plane of polarization is rotated in either a clockwise
(positive) or counter-clockwise (negative) direction, and the analyzer must be turned an appropriate matching angle, α, if full light
intensity is to reach the detector. In the above illustration, the sample has rotated the polarization plane clockwise by +90º, and the
analyzer has been turned this amount to permit maximum light transmission.
The observed rotations (α) of enantiomers are opposite in direction. One enantiomer will rotate polarized light in a clockwise
direction, termed dextrorotatory or (+), and its mirror-image partner in a counter-clockwise manner, termed levorotatory or (–). The
prefixes dextro and levo come from the Latin dexter, meaning right, and laevus, for left, and are abbreviated d and l respectively. If
equal quantities of each enantiomer are examined , using the same sample cell, then the magnitude of the rotations will be the same,
with one being positive and the other negative. To be absolutely certain whether an observed rotation is positive or negative it is often
necessary to make a second measurement using a different amount or concentration of the sample. In the above illustration, for
example, α might be –90º or +270º rather than +90º. If the sample concentration is reduced by 10%, then the positive rotation would
change to +81º (or +243º) while the negative rotation would change to –81º, and the correct α would be identified unambiguously.
Since it is not always possible to obtain or use samples of exactly the same size, the observed rotation is usually corrected to
compensate for variations in sample quantity and cell length. Thus it is common practice to convert the observed rotation, α, to a
specific rotation, by the following formula:
α
[α]D = (5.3.1)
lc

where
[α]D is the specific rotation
l is the cell length in dm

c is the concentration in g/ml

D designates that the light used is the 589 line from a sodium lamp

Compounds that rotate the plane of polarized light are termed optically active. Each enantiomer of a stereoisomeric pair is optically
active and has an equal but opposite-in-sign specific rotation. Specific rotations are useful in that they are experimentally determined
constants that characterize and identify pure enantiomers. For example, the lactic acid and carvone enantiomers discussed earlier have
the following specific rotations.
Carvone from caraway: [α]D = +62.5º this isomer may be referred to as (+)-carvone or d-carvone
Carvone from spearmint: [α]D = –62.5º this isomer may be referred to as (–)-carvone or l-carvone
Lactic acid from muscle tissue: [α]D = +2.5º this isomer may be referred to as (+)-lactic acid or d-lactic acid
Lactic acid from sour milk: [α]D = –2.5º this isomer may be referred to as (–)-lactic acid or l-lactic acid

A 50:50 mixture of enantiomers has no observable optical activity. Such mixtures are called racemates or racemic modifications, and
are designated (±). When chiral compounds are created from achiral compounds, the products are racemic unless a single enantiomer
of a chiral co-reactant or catalyst is involved in the reaction. The addition of HBr to either cis- or trans-2-butene is an example of
racemic product formation (the chiral center is colored red in the following equation).
CH3CH=CHCH3 + HBr (±) CH3CH2CHBrCH3

5.4.2 Updated 7/7/2019

Chiral organic compounds isolated from living organisms are usually optically active, indicating that one of the enantiomers
predominates (often it is the only isomer present). This is a result of the action of chiral catalysts we call enzymes, and reflects the
inherently chiral nature of life itself. Chiral synthetic compounds, on the other hand, are commonly racemates, unless they have been
prepared from enantiomerically pure starting materials.
There are two ways in which the condition of a chiral substance may be changed:
1. A racemate may be separated into its component enantiomers. This process is called resolution.
2. A pure enantiomer may be transformed into its racemate. This process is called racemization.

ENANTIOMERIC EXCESS
The "optical purity" is a comparison of the optical rotation of a pure sample of unknown stereochemistry versus the optical rotation of
a sample of pure enantiomer. It is expressed as a percentage. If the sample only rotates plane-polarized light half as much as expected,
the optical purity is 50%.

Because R and S enantiomers have equal but opposite optical activity, it naturally follows that a 50:50 racemic mixture of two
enantiomers will have no observable optical activity. If we know the specific rotation for a chiral molecule, however, we can easily
calculate the ratio of enantiomers present in a mixture of two enantiomers, based on its measured optical activity. When a mixture
contains more of one enantiomer than the other, chemists often use the concept of enantiomeric excess (ee) to quantify the difference.
Enantiomeric excess can be expressed as:

For example, a mixture containing 60% R enantiomer (and 40% S enantiomer) has a 20% enantiomeric excess of R: ((60-50) x 100) /
50 = 20 %.

EXAMPLE 5.3.1: CARVONE

The specific rotation of (S)-carvone is (+)61°, measured 'neat' (pure liquid sample, no solvent). The optical rotation of a neat sample
of a mixture of R and S carvone is measured at (-)23°. Which enantiomer is in excess, and what is its ee? What are the percentages
of (R)- and (S)-carvone in the sample?

Answer:
The observed rotation of the mixture is levorotary (negative, counter-clockwise), and the specific rotation of the pure S
enantiomer is given as dextrorotary (positive, clockwise), meaning that the pure R enantiomer must be levorotary, and the
mixture must contain more of the R enantiomer than of the S enantiomer.
Rotation (R/S Mix) = [Fraction(S) × Rotation (S)] + [Fraction(R) × Rotation (R)]
Let Fraction (S) = x, therefore Fraction (R) = 1 – x
Rotation (R/S Mix) = x[Rotation (S)] + (1 – x)[Rotation (R)]
–23 = x(+61) + (1 – x)(–61)
Solve for x: x = 0.3114 and (1 – x) = 0.6885
Therefore the percentages of (R)- and (S)-carvone in the sample are 68.9% and 31.1%, respectively.
ee = [(% more abundant enantiomer – 50) × 100]/50
= [68.9 – 50) × 100]/50 = 37.8%

Chiral molecules are often labeled according to the sign of their specific rotation, as in (S)-(+)-carvone and (R)-(-)-carvone, or (±)-
carvone for the racemic mixture. However, there is no relationship whatsoever between a molecule's R/S designation and the sign of its
specific rotation. Without performing a polarimetry experiment or looking in the literature, we would have no idea that (-)-carvone has
the R configuration and (+)-carvone has the S configuration.

SEPARATION OF CHIRAL COMPOUNDS

As noted earlier, chiral compounds synthesized from achiral starting materials and reagents are generally racemic (i.e. a 50:50 mixture
of enantiomers). Separation of racemates into their component enantiomers is a process called resolution. Since enantiomers have
identical physical properties, such as solubility and melting point, resolution is extremely difficult. Diastereomers, on the other hand,

5.4.3 Updated 7/7/2019

have different physical properties, and this fact is used to achieve resolution of racemates. Reaction of a racemate with an
enantiomerically pure chiral reagent gives a mixture of diastereomers, which can be separated. For example, if a racemic mixture of a
chiral alcohol is reacted with a enantiomerically pure carboxylic acid, the result is a mixture of diastereomers: in this case, because the
pure (R) entantiomer of the acid was used, the product is a mixture of (R-R) and (R-S) diastereomeric esters, which can, in theory, be
separated by their different physical properties. Subsequent hydrolysis of each separated ester will yield the 'resolved'
(enantiomerically pure) alcohols. The used in this technique are known as '

EXERCISES
1. For each of the structures indicated below, mark the chiral centres with an asterisk.

Answer:

1.
QUESTIONS
Q5.3.1
A sample with a concentration of 0.3 g/mL was placed in a cell with a length of 5 cm. The resulting rotation at the sodium D line was
+1.52°. What is the [α]D?
SOLUTIONS
S5.3.1
5 cm = 0.5 dm
[α]D = α/(c x l) = +1.52/(0.3 x 0.5) = +10.1°

5.4.4 Updated 7/7/2019

CONTRIBUTORS
Dr. Dietmar Kennepohl FCIC (Professor of Chemistry, Athabasca University)
Prof. Steven Farmer (Sonoma State University)
Organic Chemistry With a Biological Emphasis by Tim Soderberg (University of Minnesota, Morris)

5.4.5 Updated 7/7/2019

5.5: PASTEUR'S DISCOVERY OF ENANTIOMERS
OBJECTIVE
After completing this section, you should be able to discuss how the results of work carried out by Biot and Pasteur contributed to
the development of the concept of the tetrahedral carbon atom.

Because enantiomers have identical physical and chemical properties in achiral environments, separation of the stereoisomeric
components of a racemic mixture or racemate is normally not possible by the conventional techniques of distillation and
crystallization. In some cases, however, the crystal habits of solid enantiomers and racemates permit the chemist (acting as a chiral
resolving agent) to discriminate enantiomeric components of a mixture. As background for the following example, it is recommended
that the section on crystal properties be reviewed.
Tartaric acid, its potassium salt known in antiquity as "tartar", has served as the locus of several landmark events in the history of
stereochemistry. In 1832 the French chemist Jean Baptiste Biot observed that tartaric acid obtained from tartar
was optically active, rotating the plane of polarized light clockwise (dextrorotatory). An optically inactive, higher
melting, form of tartaric acid, called racemic acid was also known. A little more than a decade later, young Louis
Pasteur conducted a careful study of the crystalline forms assumed by various salts of these acids. He noticed that
under certain conditions, the sodium ammonium mixed salt of the racemic acid formed a mixture of
enantiomorphic hemihedral crystals; a drawing of such a pair is shown on the right. Pasteur reasoned that the
dissymmetry of the crystals might reflect the optical activity and dissymmetry of its component molecules. After picking the different
crystals apart with a tweezer, he found that one group yielded the known dextrorotatory tartaric acid measured by Biot; the second led
to a previously unknown levorotatory tartaric acid, having the same melting point as the dextrorotatory acid. Today we recognize that
Pasteur had achieved the first resolution of a racemic mixture, and laid the foundation of what we now call stereochemistry.
Optical activity was first observed by the French physicist Jean-Baptiste Biot. He concluded that the change in direction of plane-
polarized light when it passed through certain substances was actually a rotation of light, and that it had a molecular basis. His work
was supported by the experimentation of Louis Pasteur. Pasteur observed the existence of two crystals that were mirror images in
tartaric acid, an acid found in wine. Through meticulous experimentation, he found that one set of molecules rotated polarized light
clockwise while the other rotated light counterclockwise to the same extent. He also observed that a mixture of both, a racemic mixture
(or racemic modification), did not rotate light because the optical activity of one molecule canceled the effects of the other molecule.
Pasteur was the first to show the existence of chiral molecules.

CONTRIBUTORS
Dr. Dietmar Kennepohl FCIC (Professor of Chemistry, Athabasca University)
Prof. Steven Farmer (Sonoma State University)
William Reusch, Professor Emeritus (Michigan State U.), Virtual Textbook of Organic Chemistry

5.5.1 Updated 7/7/2019

5.6: SEQUENCE RULES FOR SPECIFYING CONFIGURATION
OBJECTIVES
After completing this section, you should be able to
1. assign Cahn-Ingold-Prelog priorities to a given set of substituents.
2. determine whether a given wedge-and-broken-line structure corresponds to an R or an S configuration, with or without the aid of
molecular models.
3. draw the wedge-and-broken-line structure for a compound, given its IUPAC name, complete with R or S designation.
4. construct a stereochemically accurate model of a given enantiomer from either a wedge-and-broken-line structure or the IUPAC
name of the compound, complete with R or S designation.

KEY TERMS
Make certain that you can define, and use in context, the key terms below.
absolute configuration
R configuration
S configuration

STUDY NOTES
When designating a structure as R or S, you must ensure that the atom or group with the lowest priority is pointing away from you,
the observer. The easiest way to show this is to use the wedge-and-broken-line representation. You can then immediately determine
whether you are observing an R configuration or an S configuration.

To name the enantiomers of a compound unambiguously, their names must include the "handedness" of the molecule. The method for
this is formally known as R/S nomenclature.

INTRODUCTION
The method of unambiguously assigning the handedness of molecules was originated by three chemists: R.S. Cahn, C. Ingold, and V.
Prelog and, as such, is also often called the Cahn-Ingold-Prelog rules. In addition to the Cahn-Ingold system, there are two ways of
experimentally determining the absolute configuration of an enantiomer:
1. X-ray diffraction analysis. Note that there is no correlation between the sign of rotation and the structure of a particular enantiomer.
2. Chemical correlation with a molecule whose structure has already been determined via X-ray diffraction.
However, for non-laboratory purposes, it is beneficial to focus on the R/S system. The sign of optical rotation, although different for
the two enantiomers of a chiral molecule,at the same temperature, cannot be used to establish the absolute configuration of an
enantiomer; this is because the sign of optical rotation for a particular enantiomer may change when the temperature changes.

STEREOCENTERS ARE LABELED R OR S

The "right hand" and "left hand" nomenclature is used to name the enantiomers of a chiral compound. The stereocenters are labeled as
R or S.

Consider the first picture: a curved arrow is drawn from the highest priority (1) substituent to the lowest priority (4) substituent. If the
arrow points in a counterclockwise direction (left when leaving the 12 o' clock position), the configuration at stereocenter is considered
S ("Sinister" → Latin= "left"). If, however, the arrow points clockwise,(Right when leaving the 12 o' clock position) then the
stereocenter is labeled R ("Rectus" → Latin= "right"). The R or S is then added as a prefix, in parenthesis, to the name of the
enantiomer of interest.

EXAMPLE 5.5.1
(R)-2-Bromobutane

5.6.1 Updated 7/7/2019

 (S)-2,3- Dihydroxypropanal

SEQUENCE RULES TO ASSIGN PRIORITIES TO SUBSTITUENTS

Before applying the R and S nomenclature to a stereocenter, the substituents must be prioritized according to the following rules:

RULE 1
First, examine at the atoms directly attached to the stereocenter of the compound. A substituent with a higher atomic number takes
precedence over a substituent with a lower atomic number. Hydrogen is the lowest possible priority substituent, because it has the
lowest atomic number.
1. When dealing with isotopes, the atom with the higher atomic mass receives higher priority.
2. When visualizing the molecule, the lowest priority substituent should always point away from the viewer (a dashed line indicates
this). To understand how this works or looks, imagine that a clock and a pole. Attach the pole to the back of the clock, so that when
when looking at the face of the clock the pole points away from the viewer in the same way the lowest priority substituent should
point away.
3. Then, draw an arrow from the highest priority atom to the 2nd highest priority atom to the 3rd highest priority atom. Because the
4th highest priority atom is placed in the back, the arrow should appear like it is going across the face of a clock. If it is going
clockwise, then it is an R-enantiomer; If it is going counterclockwise, it is an S-enantiomer.
When looking at a problem with wedges and dashes, if the lowest priority atom is not on the dashed line pointing away, the molecule
must be rotated.
Remember that
Wedges indicate coming towards the viewer.
Dashes indicate pointing away from the viewer.
RULE 2
If there are two substituents with equal rank, proceed along the two substituent chains until there is a point of difference. First,
determine which of the chains has the first connection to an atom with the highest priority (the highest atomic number). That chain has
the higher priority.
If the chains are similar, proceed down the chain, until a point of difference.
For example: an ethyl substituent takes priority over a methyl substituent. At the connectivity of the stereocenter, both have a carbon
atom, which are equal in rank. Going down the chains, a methyl has only has hydrogen atoms attached to it, whereas the ethyl has
another carbon atom. The carbon atom on the ethyl is the first point of difference and has a higher atomic number than hydrogen;
therefore the ethyl takes priority over the methyl.

RULE 3
If a chain is connected to the same kind of atom twice or three times, check to see if the atom it is connected to has a greater atomic
number than any of the atoms that the competing chain is connected to.
If none of the atoms connected to the competing chain(s) at the same point has a greater atomic number: the chain bonded to the
same atom multiple times has the greater priority
If however, one of the atoms connected to the competing chain has a higher atomic number: that chain has the higher priority.

EXAMPLE 5.5.2
A 1-methylethyl substituent takes precedence over an ethyl substituent. Connected to the first carbon atom, ethyl only has one other
carbon, whereas the 1-methylethyl has two carbon atoms attached to the first; this is the first point of difference. Therefore, 1-

5.6.2 Updated 7/7/2019

methylethyl ranks higher in priority than ethyl, as shown below:

However:

Remember that being double or triple bonded to an atom means that the atom is connected to the same atom twice. In such a case,
follow the same method as above.

Caution!!
Keep in mind that priority is determined by the first point of difference along the two similar substituent chains. After the first point
of difference, the rest of the chain is irrelevant.

When looking for the first point of difference on similar substituent chains, one may encounter branching. If there is branching,
choose the branch that is higher in priority. If the two substituents have similar branches, rank the elements within the branches
until a point of difference.

5.6.3 Updated 7/7/2019

 After all your substituents have been prioritized in the correct manner, you can now name/label the molecule R or S.
1. Put the lowest priority substituent in the back (dashed line).
2. Proceed from 1 to 2 to 3. (it is helpful to draw or imagine an arcing arrow that goes from 1--> 2-->3)
3. Determine if the direction from 1 to 2 to 3 clockwise or counterclockwise.
i) If it is clockwise it is R.
ii) if it is counterclockwise it is S.

USE YOUR MODELING KIT: Models assist in visualizing the structure. When using a model, make sure the lowest priority is
pointing away from you. Then determine the direction from the highest priority substituent to the lowest: clockwise (R) or
counterclockwise (S).
IF YOU DO NOT HAVE A MODELING KIT: remember that the dashes mean the bond is going into the screen and the wedges
means that bond is coming out of the screen. If the lowest priority bond is not pointing to the back, mentally rotate it so that it is.
However, it is very useful when learning organic chemistry to use models.

PROBLEMS
Are the following R or S?

SOLUTIONS
1. S: I > Br > F > H. The lowest priority substituent, H, is already going towards the back. It turns left going from I to Br to F, so it's a
S.
2. R: Br > Cl > CH3 > H. You have to switch the H and Br in order to place the H, the lowest priority, in the back. Then, going from
Br to Cl, CH3 is turning to the right, giving you a R.
3. Neither R or S: This molecule is achiral. Only chiral molecules can be named R or S.
4. R: OH > CN > CH2NH2 > H. The H, the lowest priority, has to be switched to the back. Then, going from OH to CN to CH2NH2,
you are turning right, giving you a R.
5. (5) S: −COOH > −CH OH > C≡CH > H. Then, going from −COOH to −CH OH to −C≡CH you are turning left, giving
2 2

you a S configuration.

OUTSIDE LINKS
http://www.youtube.com/watch?v=EphUiPiQiCo
http://en.wikipedia.org/wiki/Absolute_configuration

5.6.4 Updated 7/7/2019

REFERENCES
1. Schore and Vollhardt. Organic Chemistry Structure and Function. New York:W.H. Freeman and Company, 2007.
2. McMurry, John and Simanek, Eric. Fundamentals of Organic Chemistry. 6th Ed. Brooks Cole, 2006.

EXERCISES
QUESTIONS
Q5.5.1
Orient the following so that the least priority (4) atom is paced behind, then assign stereochemistry (R or S).

Q5.5.2
Draw (R)-2-bromobutan-2-ol.
Q5.5.3
Assign R/S to the following molecule.

SOLUTIONS
S5.5.1

A = S; B = R
S5.5.2

S5.5.3
The stereo center is R.

CONTRIBUTORS
Ekta Patel (UCD), Ifemayowa Aworanti (University of Maryland Baltimore County)
Dr. Dietmar Kennepohl FCIC (Professor of Chemistry, Athabasca University)
Prof. Steven Farmer (Sonoma State University)

5.6.5 Updated 7/7/2019

5.7: DIASTEREOMERS
OBJECTIVES
After completing this section, you should be able to
1. calculate the maximum number of stereoisomers possible for a compound containing a specified number of chiral carbon atoms.
2. draw wedge-and-broken-line structures for all possible stereoisomers of a compound containing two chiral carbon atoms, with
or without the aid of molecular models.
3. assign R,S configurations to wedge-and-broken-line structures containing two chiral carbon atoms, with or without the aid of
molecular models.
4. determine, with or without the aid of molecular models, whether two wedge-and-broken-line structures containing two chiral
carbon atoms are identical, represent a pair of enantiomers, or represent a pair of diastereomers.
5. draw the wedge-and-broken-line structure of a specific stereoisomer of a compound containing two chiral carbon atoms, given
its IUPAC name and R,S configuration.

KEY TERMS
Make certain that you can define, and use in context, the key term below.
diastereomer

Diastereomers are stereoisomers that are not related as object and mirror image and are not enantiomers. Unlike enatiomers which are
mirror images of each other and non-sumperimposable, diastereomers are not mirror images of each other and non-
superimposable. Diastereomers can have different physical properties and reactivity. They have different melting points and boiling
points and different densities. They have two or more stereocenters.

INTRODUCTION
It is easy to mistake between diasteromers and enantiomers. For example, we have four steroisomers of 3-bromo-2-butanol. The four
possible combination are SS, RR, SR and RS (Figure 5.6.1). One of the molecule is the enantiomer of its mirror image molecule and
diasteromer of each of the other two molecule (SS is enantiomer of RR and diasteromer of RS and SR). SS's mirror image is RR and
they are not superimposable, so they are enantiomers. RS and SR are not mirror image of SS and are not superimposable to each other,
so they are diasteromers.

Figure 5.6.1

DIASTEREOMERS VS. ENANTIOMERS

5.7.1 Updated 7/7/2019

Tartaric acid, C4H6O6, is an organic compound that can be found in grape, bananas, and in wine. The structures of tartaric acid itself is
really interesting. Naturally, it is in the form of (R,R) stereocenters. Artificially, it can be in the meso form (R,S), which is achiral. R,R
tartaric acid is enantiomer to is mirror image which is S,S tartaric acid and diasteromers to meso-tartaric acid (Figure 5.6.2).
(R,R) and (S,S) tartaric acid have similar physical properties and reactivity. However, meso-tartaric acid have different physical
properties and reactivity. For example, melting point of (R,R) & (S,S) tartaric is about 170 degree Celsius, and melting point of meso-
tartaric acid is about 145 degree Celsius.

Figure 5.6.2
We turn our attention next to molecules which have more than one stereocenter. We will start with a common four-carbon sugar called
D-erythrose.

A note on sugar nomenclature: biochemists use a special system to refer to the stereochemistry of sugar molecules, employing names
of historical origin in addition to the designators 'D' and 'L'. You will learn about this system if you take a biochemistry class. We will
use the D/L designations here to refer to different sugars, but we won't worry about learning the system.
As you can see, D-erythrose is a chiral molecule: C2 and C3 are stereocenters, both of which have the R configuration. In addition, you
should make a model to convince yourself that it is impossible to find a plane of symmetry through the molecule, regardless of the
conformation. Does D-erythrose have an enantiomer? Of course it does – if it is a chiral molecule, it must. The enantiomer of erythrose
is its mirror image, and is named L-erythrose (once again, you should use models to convince yourself that these mirror images of
erythrose are not superimposable).

Notice that both chiral centers in L-erythrose both have the S configuration.

NOTE
In a pair of enantiomers, all of the chiral centers are of the opposite configuration.

What happens if we draw a stereoisomer of erythrose in which the configuration is S at C2 and R at C3? This stereoisomer, which is a
sugar called D-threose, is not a mirror image of erythrose. D-threose is a diastereomer of both D-erythrose and L-erythrose.

The definition of diastereomers is simple: if two molecules are stereoisomers (same molecular formula, same connectivity, different
arrangement of atoms in space) but are not enantiomers, then they are diastereomers by default. In practical terms, this means that at

5.7.2 Updated 7/7/2019

least one - but not all - of the chiral centers are opposite in a pair of diastereomers. By definition, two molecules that are
diastereomers are not mirror images of each other.
L-threose, the enantiomer of D-threose, has the R configuration at C2 and the S configuration at C3. L-threose is a diastereomer of both
erythrose enantiomers.
In general, a structure with n stereocenters will have 2n different stereoisomers. (We are not considering, for the time being, the
stereochemistry of double bonds – that will come later). For example, let's consider the glucose molecule in its open-chain form (recall
that many sugar molecules can exist in either an open-chain or a cyclic form). There are two enantiomers of glucose, called D-glucose
and L-glucose. The D-enantiomer is the common sugar that our bodies use for energy. It has n = 4 stereocenters, so therefore there are
2n = 24 = 16 possible stereoisomers (including D-glucose itself).

In L-glucose, all of the stereocenters are inverted relative to D-glucose. That leaves 14 diastereomers of D-glucose: these are molecules
in which at least one, but not all, of the stereocenters are inverted relative to D-glucose. One of these 14 diastereomers, a sugar called
D-galactose, is shown above: in D-galactose, one of four stereocenters is inverted relative to D-glucose. Diastereomers which differ in
only one stereocenter (out of two or more) are called epimers. D-glucose and D-galactose can therefore be refered to as epimers as
well as diastereomers.

EXAMPLE 5.6.1
Draw the structure of L-galactose, the enantiomer of D-galactose.
Draw the structure of two more diastereomers of D-glucose. One should be an epimer.

Answer:

Erythronolide B, a precursor to the 'macrocyclic' antibiotic erythromycin, has 10 stereocenters. It’s enantiomer is that molecule in
which all 10 stereocenters are inverted.

In total, there are 210 = 1024 stereoisomers in the erythronolide B family: 1022 of these are diastereomers of the structure above, one is
the enantiomer of the structure above, and the last is the structure above.
We know that enantiomers have identical physical properties and equal but opposite degrees of specific rotation. Diastereomers, in
theory at least, have different physical properties – we stipulate ‘in theory’ because sometimes the physical properties of two or more
diastereomers are so similar that it is very difficult to separate them. In addition, the specific rotations of diastereomers are unrelated –
they could be the same sign or opposite signs, and similar in magnitude or very dissimilar.

EXERCISES
QUESTIONS
Q5.6.1

5.7.3 Updated 7/7/2019

Determine the stereochemistry of the following molecule:

SOLUTIONS
S5.6.1

CONTRIBUTORS
Organic Chemistry With a Biological Emphasis by Tim Soderberg (University of Minnesota, Morris)
Dr. Dietmar Kennepohl FCIC (Professor of Chemistry, Athabasca University)

5.7.4 Updated 7/7/2019

5.8: MESO COMPOUNDS
OBJECTIVES
After completing this section, you should be able to
1. determine whether or not a compound containing two chiral carbon atoms will have a meso form, given its Kekulé, condensed
or shorthand structure, or its IUPAC name.
2. draw wedge-and-broken-line structures for the enantiomers and meso form of a compound such as tartaric acid, given its IUPAC
name, or its Kekulé, condensed or shorthand structure.
3. make a general comparison of the physical properties of the enantiomers, meso form and racemic mixture of a compound such
as tartaric acid.

KEY TERMS
Make certain that you can define, and use in context, the key term below.
meso compound

STUDY NOTES
You may be confused by the two sets of structures showing “rotations.” Of course in each case the two structures shown are
identical, they represent the same molecule looked at from two different perspectives. In the first case, there is a 120° rotation
around the single carbon-carbon bond. In the second, the whole molecule is rotated 180° top to bottom.

Meso Compounds
A meso compound is an achiral compound that has chiral centers. It is superimposed on its mirror image and is optically inactive
although it contains two or more stereocenters.

INTRODUCTION
In general, a meso compound should contain two or more identical substituted stereocenters. Also, it has an internal symmetry plane
that divides the compound in half. These two halves reflect each other by the internal mirror. The stereochemistry of stereocenters
should "cancel out". What it means here is that when we have an internal plane that splits the compound into two symmetrical sides,
the stereochemistry of both left and right side should be opposite to each other, and therefore, result in optically inactive. Cyclic
compounds may also be meso.

IDENTIFICATION
If A is a meso compound, it should have two or more stereocenters, an internal plane, and the stereochemistry should be R and S.
1. Look for an internal plane, or internal mirror, that lies in between the compound.
2. The stereochemistry (e.g. R or S) is very crucial in determining whether it is a meso compound or not. As mentioned above, a meso
compound is optically inactive, so their stereochemistry should cancel out. For instance, R cancels S out in a meso compound with
two stereocenters.

trans-1,2-dichloro-1,2-ethanediol

5.8.1 Updated 7/7/2019

 (meso)-2,3-dibromobutane
Tips: An interesting thing about single bonds or sp3-orbitals is that we can rotate the substituted groups that attached to a stereocenter
around to recognize the internal plane. As the molecule is rotated, its stereochemistry does not change. For