Organic Chemistry

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1: Structure and Bonding

1.0: Introduction to Organic Chemistry
1.1: Atomic Structure - The Nucleus
1.2: Atomic Structure - Orbitals
1.3: Atomic Structure - Electron Con gurations
1.4: Development of Chemical Bonding Theory
1.5: Describing Chemical Bonds - Valence Bond Theory
1.6: sp³ Hybrid Orbitals and the Structure of Methane
1.7: sp³ Hybrid Orbitals and the Structure of Ethane
1.8: sp² Hybrid Orbitals and the Structure of Ethylene
1.9: sp Hybrid Orbitals and the Structure of Acetylene
1.10: Hybridization of Nitrogen, Oxygen, Phosphorus and Sulfur
1.11: Describing Chemical Bonds - Molecular Orbital Theory
1.12: Drawing Chemical Structures
1.S: Structure and Bonding (Summary)

2: Polar Covalent Bonds; Acids and Bases

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 De nition
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 De nition
2.12: Noncovalent Interactions Between Molecules
2.MM: Molecular Models
2.S: Polar Covalent Bonds; Acids and Bases (Summary)

3: Organic Compounds- Alkanes and Their Stereochemistry

3.1: Functional Groups
3.2: Alkanes and Alkane Isomers
3.3: Alkyl Groups
3.4: Naming Alkanes
3.5: Properties of Alkanes
3.6: Conformations of Ethane
3.7: Conformations of Other Alkanes
3.8: Gasoline - A Deeper Look
3.S: Organic Compounds- Alkanes and Their Stereochemistry (Summary)

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4: Organic Compounds - Cycloalkanes and their Stereochemistry
4.1: Naming Cycloalkanes
4.2: Cis-Trans Isomerism in Cycloalkanes
4.3: Stability of Cycloalkanes - Ring Strain
4.4: Conformations of Cycloalkanes
4.5: Conformations of Cyclohexane
4.6: Axial and Equatorial Bonds in Cyclohexane
4.7: Conformations of Monosubstituted Cyclohexanes
4.8: Conformations of Disubstituted Cyclohexanes
4.9: Conformations of Polycyclic Molecules
4.S: Organic Compounds- Cycloalkanes and their Stereochemistry (Summary)

5: Stereochemistry at Tetrahedral Centers

5.0: Chapter Objectives and Introduction
5.1: Enantiomers and the Tetrahedral Carbon
5.2: The Reason for Handedness in Molecules - Chirality
5.3: Optical Activity
5.4: Pasteur's Discovery of Enantiomers
5.5: Sequence Rules for Specifying Con guration
5.6: Diastereomers
5.7: Meso Compounds
5.8: Racemic Mixtures and the Resolution of Enantiomers
5.9: A Review of Isomerism
5.10: Chirality at Nitrogen, Phosphorus, and Sulfur
5.11: Prochirality
5.12: Chirality in Nature and Chiral Environments
5.S: Stereochemistry at Tetrahedral Centers (Summary)
5.xx: Enantiomers and Diastereomers

6: An Overview of Organic Reactions

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

7: Alkenes- Structure and Reactivity

7.1: Introduction to Alkenes
7.2: Industrial Preparation and Use of Alkenes
7.3: Calculating Degree of Unsaturation
7.4: Naming Alkenes
7.5: Cis-Trans Isomerism in Alkenes
7.6: Sequence Rules - The E,Z Designation

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 7.7: Stability of Alkenes
7.8: Electrophilic Addition Reactions of Alkenes
7.9: Orientation of Electrophilic Additions - Markovnikov's Rule
7.10: Carbocation Structure and Stability
7.11: The Hammond Postulate
7.12: Evidence for the Mechanism of Electrophilic Additions - Carbocation Rearrangements
7.S: Alkenes- Structure and Reactivity (Summary)

8: Alkenes- Reactions and Synthesis

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

9: Alkynes - An Introduction to Organic Synthesis

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

10: Organohalides
10.0: Introduction to Organohalides
10.1: Names and Properties of Alkyl Halides
10.2: Preparing Alkyl Halides from Alkanes - Radical Halogenation
10.3: Preparing Alkyl Halides from Alkenes - Allylic Bromination
10.4: Stability of the Allyl Radical - Resonance Revisited
10.5: Preparing Alkyl Halides from Alcohols
10.6: Reactions of Alkyl Halides - Grignard Reagents
10.7: Organometallic Coupling Reactions
10.8: Oxidation and Reduction in Organic Chemistry
10.S: Organohalides (Summary)

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11: Reactions of Alkyl Halides- Nucleophilic Substitutions and Eliminations
11.0: Introduction
11.1: The Discovery of Nucleophilic Substitution Reactions
11.2: The SN2 Reaction
11.3: Characteristics of the SN2 Reaction
11.4: The SN1 Reaction
11.5: Characteristics of the SN1 Reaction
11.6: Biological Substitution Reactions
11.7: Elimination Reactions- Zaitsev's Rule
11.8: The E2 Reaction and the Deuterium Isotope Effect
11.9: The E2 Reaction and Cyclohexane Conformation
11.10: The E1 and E1cB Reactions
11.11: Biological Elimination Reactions
11.12: A Summary of Reactivity - SN1, SN2, E1, E1cB, and E2
11.S: Reactions of Alkyl Halides - Nucleophilic Substitutions and Eliminations (Summary)

12: Structure Determination - Mass Spectrometry and Infrared

Spectroscopy
12.0: Introduction
12.1: Mass Spectrometry of Small Molecules - Magnetic-Sector Instruments
12.2: Interpreting Mass Spectra
12.3: Mass Spectrometry of Some Common Functional Groups
12.4: Mass Spectrometry in Biological - Time-of- ight (TOF) Instruments
12.5: Spectroscopy and the Electromagnetic Spectrum
12.6: Infrared Spectroscopy
12.7: Interpreting Infrared Spectra
12.8: Infrared Spectra of Some Common Functional Groups
12.S: Structure Determination - Mass Spectrometry and Infrared Spectroscopy (Summary)

13: Structure Determination - Nuclear Magnetic Resonance Spectroscopy

13.0: Nuclear Magnetic Resonance Spectroscopy
13.1: The Nature of NMR Absorptions
13.2: The Chemical Shift
13.3: Chemical Shifts in ¹H NMR Spectroscopy
13.4: Integration of ¹H NMR Absorptions- Proton Counting
13.5: Spin-Spin Splitting in ¹H NMR Spectra
13.6: ¹H NMR Spectroscopy and Proton Equivalence
13.7: More Complex Spin-Spin Splitting Patterns
13.8: Uses of ¹H NMR Spectroscopy
13.9: ¹³C NMR Spectroscopy - Signal Averaging and FT-NMR
13.10: Characteristics of ¹³C NMR Spectroscopy
13.11: DEPT ¹³C NMR Spectroscopy
13.12: Uses of ¹³C NMR Spectroscopy
13.S: Structure Determination - Nuclear Magnetic Resonance Spectroscopy (Summary)

14: Conjugated Compounds and Ultraviolet Spectroscopy

14.0: Introduction
14.1: Stability of Conjugated Dienes- Molecular Orbital Theory
14.2: Electrophilic Additions to Conjugated Dienes- Allylic Carbocations
14.3: Kinetic vs. Thermodynamic Control of Reactions

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 14.4: The Diels-Alder Cycloaddition Reaction
14.5: Characteristics of the Diels-Alder Reaction
14.6: Diene Polymers- Natural and Synthetic Rubbers
14.7: Structure Determination in Conjugated Systems - Ultraviolet Spectroscopy
14.8: Interpreting Ultraviolet Spectra- The Effect of Conjugation
14.9: Conjugation, Color, and the Chemistry of Vision
14.S: Conjugated Compounds and Ultraviolet Spectroscopy (Summary)

15: Benzene and Aromaticity

15.0: Introduction
15.1: Naming Aromatic Compounds
15.2: Structure and Stability of Benzene
15.3: Aromaticity and the Hückel 4n + 2 Rule
15.4: Aromatic Ions
15.5: Aromatic Heterocycles - Pyridine and Pyrrole
15.6: Polycyclic Aromatic Compounds
15.7: Spectroscopy of Aromatic Compounds
15.S: Benzene and Aromaticity (Summary)

16: Chemistry of Benzene - Electrophilic Aromatic Substitution

16.0: Introduction
16.1: Electrophilic Aromatic Substitution Reactions - Bromination
16.2: Other Aromatic Substitutions
16.3: Alkylation and Acylation of Aromatic Rings - The Friedel-Crafts Reaction
16.4: Substituent Effects in Substituted Aromatic Rings
16.5: An Explanation of Substituent Effects
16.6: Trisubstituted Benzenes - Additivity of Effects
16.7: Nucleophilic Aromatic Substitution
16.8: Benzyne
16.9: Oxidation of Aromatic Compounds
16.10: Reduction of Aromatic Compounds
16.11: Synthesis of Polysubstituted Benzenes
16.S: Chemistry of Benzene - Electrophilic Aromatic Substitution (Summary)

17: Alcohols and Phenols

17.0: Introduction to Alcohols and Phenols
17.1: Naming Alcohols and Phenols
17.2: Properties of Alcohols and Phenols
17.3: Preparation of Alcohols- A Review
17.4: Alcohols from Carbonyl Compounds- Reduction
17.5: Alcohols from Carbonyl Compounds - Grignard Reagents
17.6: Reactions of Alcohols
17.7: Oxidation of Alcohols
17.8: Protection of Alcohols
17.9: Phenols and Their Uses
17.10: Reactions of Phenols
17.11: Spectroscopy of Alcohols and Phenols
17.S: Alcohols and Phenols (Summary)

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18: Ethers and Epoxides; Thiols and Sul des
18.0: Introduction
18.1: Names and Properties of Ethers
18.2: Preparing Ethers
18.3: Reactions of Ethers- Acidic Cleavage
18.4: Reactions of Ethers- Claisen Rearrangement
18.5: Cyclic Ethers - Epoxides
18.6: Reactions of Epoxides- Ring-opening
18.7: Crown Ethers
18.8: Thiols and Sul des
18.9: Spectroscopy of Ethers
18: Interchapter- A Preview of Carbonyl Chemistry
18.S: Ethers and Epoxides; Thiols and Sul des (Summary)

19: Aldehydes and Ketones- Nucleophilic Addition Reactions

19.0: Chapter Objectives and Preview of Carbonyl Chemistry
19.1: Naming Aldehydes and Ketones
19.2: Preparing Aldehydes and Ketones
19.3: Oxidation of Aldehydes and Ketones
19.4: Nucleophilic Addition Reactions of Aldehydes and Ketones
19.5: Nucleophilic Addition of Water- Hydration
19.6: Nucleophilic Addition of HCN- Cyanohydrin Formation
19.7: Nucleophilic Addition of Hydride and Grignard Reagents- Alcohol Formation
19.8: Nucleophilic Addition of Amines- Imine and Enamine Formation
19.9: Nucleophilic Addition of Hydrazine - The Wolff-Kishner Reaction
19.10: Nucleophilic Addition of Alcohols- Acetal Formation
19.11: Nucleophilic Addition of Phosphorus Ylides- The Wittig Reaction
19.12: Biological Reductions
19.13: Conjugate Nucleophilic Addition to alpha, beta-unsaturated Aldehydes and Ketones
19.14: Spectroscopy of Aldehydes and Ketones
19.S: Aldehydes and Ketones (Summary)

20: Carboxylic Acids and Nitriles

20.0: Chapter Objectives and Introduction to Carboxylic Acids
20.1: Naming Carboxylic Acids and Nitriles
20.2: Structure and Properties of Carboxylic Acids
20.3: Biological Acids and the Henderson-Hasselbalch Equation
20.4: Substituent Effects on Acidity
20.5: Preparing Carboxylic Acids
20.6: Reactions of Carboxylic Acids - An Overview
20.7: Chemistry of Nitriles
20.8: Spectroscopy of Carboxylic Acids and Nitriles
20.S: Carboxylic Acids and Nitriles (Summary)

21: Carboxylic Acid Derivatives- Nucleophilic Acyl Substitution Reactions

21.0: Chapter Objectives and Introduction to Carboxylic Acid Derivatives
21.1: Naming Carboxylic Acid Derivatives
21.2: Nucleophilic Acyl Substitution Reactions
21.3: Nucleophilic Acyl Substitution Reactions of Carboxylic Acids
21.4: Chemistry of Acid Halides

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 21.5: Chemistry of Acid Anhydrides
21.6: Chemistry of Esters
21.7: Chemistry of Amides
21.8: Chemistry of Thioesters and Acyl Phosphates - Biological Carboxylic Acid Derivatives
21.9: Polyamides and Polyesters- Step-Growth Polymers
21.10: Spectroscopy of Carboxylic Acid Derivatives
21.S: Carboxylic Acid Derivatives (Summary)

22: Carbonyl Alpha-Substitution Reactions

22.0: Chapter Objectives and Introduction to Carbonyl Alpha-Substitution Reactions
22.1: Keto-Enol Tautomerism
22.2: Reactivity of Enols: The Mechanism of Alpha-Substitution Reactions
22.3: Alpha Halogenation of Aldehydes and Ketones
22.4: Alpha Bromination of Carboxylic Acids
22.5: Acidity of Alpha Hydrogen Atoms: Enolate Ion Formation
22.6: Reactivity of Enolate Ions
22.7: Alkylation of Enolate Ions
22.S: Carbonyl Alpha-Substitution Reactions (Summary)

23: Carbonyl Condensation Reactions

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

24: Amines and Heterocycles

24.1: Naming Amines
24.2: Structure and Properties of Amines
24.3: Basicity of Amines
24.4: Basicity of Arylamines
24.5: Biological Amines and the Henderson-Hasselbalch Equation
24.6: Synthesis of Amines
24.7: Reactions of Amines
24.8: Reactions of Arylamines
24.9: Heterocyclic Amines
24.10: Spectroscopy of Amines
24.S: Amines and Heterocycles (Summary)

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25: Biomolecules- Carbohydrates
25.0: Introduction
25.1: Classi cation of Carbohydrates
25.2: Depicting Carbohydrate Stereochemistry - Fischer Projections
25.3: D, L Sugars
25.4: Con gurations of Aldoses
25.5: Cyclic Structures of Monosaccharides - Anomers
25.6: Reactions of Monosaccharides
25.7: The Eight Essential Monosaccharides
25.8: Disaccharides
25.9: Polysaccharides and Their Synthesis
25.10: Other Important Carbohydrates
25.11: Cell-Surface Carbohydrates and In uenza Viruses
25.S: Biomolecules- Carbohydrates (Summary)

26: Biomolecules- Amino Acids, Peptides, and Proteins

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

27: Biomolecules - Lipids

27.0: Introduction to Lipids
27.1: Waxes, Fats, and Oils
27.2: Soap
27.3: Phospholipids
27.4: Prostaglandins and Other Eicosanoids
27.5: Terpenoids
27.6: Steroids
27.7: Biosynthesis of Steroids
27.S: Biomolecules - Lipids (Summary)

28: Biomolecules - Nucleic Acids

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

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Chapter 30: Orbitals and Organic Chemistry - Pericyclic Reactions
30.1: Molecular Orbitals of Conjugated Pi Systems
30.2: Electrocyclic Reactions
30.3: Stereochemistry of Thermal Electrocyclic Reactions
30.4: Photochemical Electrocyclic Reactions
30.5: Cycloaddition Reactions
30.6: Stereochemistry of Cycloadditions
30.7: Sigmatropic Rearrangements
30.8: Some Examples of Sigmatropic Rearrangements
30.9: A Summary of Rules for Pericyclic Reactions

Chapter 31: Synthetic Polymers

31.1: Chain-Growth Polymers
31.2: Stereochemistry of Polymerization: Ziegler-Natta Catalysts
31.3: Copolymers
31.4: Step-Growth Polymers
31.5: Ole n Metathesis Polymerization
31.6: Polymer Structure and Physical Properties

Index
Detailed Licensing

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 CHAPTER OVERVIEW
1: Structure and Bonding
 Chapter Objectives

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.

1.0: Introduction to Organic Chemistry

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

1: Structure and Bonding is shared under a CC BY-SA 4.0 license and was authored, remixed, and/or curated by Steven Farmer & Dietmar
Kennepohl.

1
1.0: Introduction to Organic Chemistry
 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.

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)
Jöns Jacob Berzelius, a physician by trade, first coined the term “organic chemistry” in 1806 for the study of compounds derived
from biological sources. Up through the early 19th century, naturalists and scientists observed critical differences between
compounds that were derived from living things and those that were not.

In 1828, Friedrich Wöhler (widely regarded as a pioneer in organic chemistry) successfully completed an organic synthesis by
heating ammonium cyanate and synthesizing of the biological compound urea (a component of urine in many animals) in what is
now called “the Wöhler synthesis.” Until this discovery it was widely believed by chemists that organic substances could only be
formed under the influence of the “vital force” in the bodies of animals and plants. Wöhler’s synthesis dramatically proved that
view to be false.
O
heat
NH4 NCO C
H2 N NH2
ammonium cyanate urea

Urea synthesis was a critical discovery for biochemists because it showed that a compound known to be produced in nature only by
biological organisms could be produced in a laboratory under controlled conditions from inanimate matter. This “in vitro” synthesis

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of organic matter disproved the common theory (vitalism) about the vis vitalis, a transcendent “life force” needed for producing
organic compounds.
The ability to manipulate organic compounds includes fermentation to create wine and the making of soap, both of which have
been a part of society so long their discovery has been lost in antiquity. Evidence has shown the Babylonians, as early as 2800 BC,
were creating soap by mixing animal fat with wood ashes. It wasn't until the 19th century that the chemical nature of the creation of
soap was discovered by Eugène Chevreul. In a reaction now call saponification, fats are heated in the presence of a strong base
(KOH or NaOH) to produce fatty acid salts and glycerol. The fatty acid salts are the soap which improve water's ability to dissolve
grease.
NaOH
animal fat soap + glycerol
H 2O

Although originally defined as the chemistry of biological molecules, organic chemistry has since been redefined to refer
specifically to carbon compounds — even those with non-biological origin. Some carbon molecules are not considered organic,
with carbon dioxide being the most well known and most common inorganic carbon compound, but such molecules are the
exception and not the rule. Organic chemistry focuses on carbon compounds and following movement of the electrons in carbon
chains and rings, and also how electrons are shared with other carbon atoms and heteroatoms. Organic chemistry is primarily
concerned with the properties of covalent bonds and non-metallic elements, though ions and metals do play critical roles in some
reactions.
Why is carbon so special? The answer to this question involves carbon's special ability to bond with itself, which will be discussed
in this chapter. Carbon is unique in its ability to form a wide variety of compounds from simple to complex. There are literally
millions of organic compounds known to science from methane, which contains one carbon atom, to DNA which contains millions
of carbons. More importantly, organic chemistry gives us the ability to make and alter the structure of organic compounds, which is
the main topic in this book. The applications of organic chemistry are myriad, and include all sorts of plastics, dyes, flavorings,
scents, detergents, explosives, fuels and many, many other products. Read the ingredient list for almost any kind of food that you
eat — or even your shampoo bottle — and you will see the handiwork of organic chemists listed there.

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. The field of
organic chemistry is probably the most active and important field of chemistry at the moment, due to its extreme applicability to
both biochemistry (especially in the pharmaceutical industry) and petrochemistry (especially in the energy industry). Organic
chemistry has a relatively recent history, but it will have an enormously important future, affecting the lives of everyone around the
world for many, many years to come

1.0: Introduction to Organic Chemistry is shared under a CC BY-SA 4.0 license and was authored, remixed, and/or curated by Steven Farmer,
Dietmar Kennepohl, Krista Cunningham, OpenStax, & OpenStax.

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1.1: 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.

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. 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.

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.
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

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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 (1.1.1)

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

Elements
To date, about 115 different elements have been discovered; by definition, each is chemically unique. To understand why they are
unique, you need to understand the structure of the atom (the fundamental, individual particle of an element) and the characteristics
of its components. Atoms consist of electrons, protons, and neutrons. Although this is an oversimplification that ignores the other
subatomic particles that have been discovered, it is sufficient for discussion of chemical principles. Some properties of these
subatomic particles are summarized in Table 1.1.1, which illustrates three important points:
1. Electrons and protons have electrical charges that are identical in magnitude but opposite in sign. Relative charges of −1 and +1
are assigned to the electron and proton, respectively.
2. Neutrons have approximately the same mass as protons but no charge. They are electrically neutral.
3. The mass of a proton or a neutron is about 1836 times greater than the mass of an electron. Protons and neutrons constitute the
bulk of the mass of atoms.
The discovery of the electron and the proton was crucial to the development of the modern model of the atom and provides an
excellent case study in the application of the scientific method. In fact, the elucidation of the atom’s structure is one of the greatest
detective stories in the history of science.
Table 1.1.1 : Properties of Subatomic Particles*
Electrical Charge
Particle Mass (g) Atomic Mass (amu) Relative Charge
(coulombs)

electron 9.109 × 10
−28
0.0005486 −1.602 × 10−19 −1

proton 1.673 × 10
−24
1.007276 +1.602 × 10−19 +1

neutron 1.675 × 10
−24
1.008665 0 0

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In most cases, the symbols for the elements are derived directly from each element’s name, such as C for carbon, U for uranium, Ca
for calcium, and Po for polonium. Elements have also been named for their properties [such as radium (Ra) for its radioactivity],
for the native country of the scientist(s) who discovered them [polonium (Po) for Poland], for eminent scientists [curium (Cm) for
the Curies], for gods and goddesses [selenium (Se) for the Greek goddess of the moon, Selene], and for other poetic or historical
reasons. Some of the symbols used for elements that have been known since antiquity are derived from historical names that are no
longer in use; only the symbols remain to indicate their origin. Examples are Fe for iron, from the Latin ferrum; Na for sodium,
from the Latin natrium; and W for tungsten, from the German wolfram. Examples are in Table 1.1.2.
Table 1.1.2 : Element Symbols Based on Names No Longer in Use
Element Symbol Derivation Meaning

antimony Sb stibium Latin for “mark”

from Cyprium, Latin name for the

island of Cyprus, the major source
copper Cu cuprum
of copper ore in the Roman
Empire

gold Au aurum Latin for “gold”

iron Fe ferrum Latin for “iron”

lead Pb plumbum Latin for “heavy”

mercury Hg hydrargyrum Latin for “liquid silver”

potassium K kalium from the Arabic al-qili, “alkali”

silver Ag argentum Latin for “silver”

sodium Na natrium Latin for “sodium”

tin Sn stannum Latin for “tin”

German for “wolf stone” because

it interfered with the smelting of
tungsten W wolfram
tin and was thought to devour the
tin

Recall that the nuclei of most atoms contain neutrons as well as protons. Unlike protons, the number of neutrons is not absolutely
fixed for most elements. Atoms that have the same number of protons, and hence the same atomic number, but different numbers of
neutrons are called isotopes. All isotopes of an element have the same number of protons and electrons, which means they exhibit
the same chemistry. The isotopes of an element differ only in their atomic mass, which is given by the mass number (A), the sum of
the numbers of protons and neutrons.

Carbon Isotopes
The element carbon (C) has an atomic number of 6, which means that all neutral carbon atoms contain 6 protons and 6 electrons. In
a typical sample of carbon-containing material, 98.89% of the carbon atoms also contain 6 neutrons, so each has a mass number of
12. An isotope of any element can be uniquely represented as X , where X is the atomic symbol of the element. The isotope of
A
Z

carbon that has 6 neutrons is therefore C . The subscript indicating the atomic number is actually redundant because the atomic
12
6

symbol already uniquely specifies Z. Consequently, C is more often written as 12C, which is read as “carbon-12.” Nevertheless,
12
6

the value of Z is commonly included in the notation for nuclear reactions because these reactions involve changes in Z.

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 Figure 1.1.2 : Formalism used for identifying specific nuclide (any particular kind of nucleus)
In addition to C , a typical sample of carbon contains 1.11% C (13C), with 7 neutrons and 6 protons, and a trace of C (14C),
12 13
6
14
6

with 8 neutrons and 6 protons. The nucleus of 14C is not stable, however, but undergoes a slow radioactive decay that is the basis of
the carbon-14 dating technique used in archaeology. Many elements other than carbon have more than one stable isotope; tin, for
example, has 10 isotopes. The properties of some common isotopes are in Table 1.1.3.
Table 1.1.3 : Properties of Selected Isotopes
Isotope Mass Isotope Masses Percent Abundances
Element Symbol Atomic Mass (amu)
Number (amu) (%)

1 1.007825 99.9855
hydrogen H 1.0079
2 2.014102 0.0115

10 10.012937 19.91
boron B 10.81
11 11.009305 80.09

12 12 (defined) 99.89
carbon C 12.011
13 13.003355 1.11

16 15.994915 99.757

oxygen O 15.9994 17 16.999132 0.0378

18 17.999161 0.205

54 53.939611 5.82

56 55.934938 91.66
iron Fe 55.845
57 56.935394 2.19

58 57.933276 0.33

234 234.040952 0.0054

uranium U 238.03 235 235.043930 0.7204

238 238.050788 99.274

Sources of isotope data: G. Audi et al., Nuclear Physics A 729 (2003): 337–676; J. C. Kotz and K. F. Purcell, Chemistry and
Chemical Reactivity, 2nd ed., 1991.

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  Example 1.1.1

An element with three stable isotopes has 82 protons. The separate isotopes contain 124, 125, and 126 neutrons. Identify the
element and write symbols for the isotopes.
Given: number of protons and neutrons
Asked for: element and atomic symbol
Strategy:
A. Refer to the periodic table and use the number of protons to identify the element.
B. Calculate the mass number of each isotope by adding together the numbers of protons and neutrons.
C. Give the symbol of each isotope with the mass number as the superscript and the number of protons as the subscript, both
written to the left of the symbol of the element.
Solution:
A The element with 82 protons (atomic number of 82) is lead: Pb.
B For the first isotope, A = 82 protons + 124 neutrons = 206. Similarly, A = 82 + 125 = 207 and A = 82 + 126 = 208 for the
second and third isotopes, respectively. The symbols for these isotopes are P b, P b , and
206
82
207
82
P b , which are usually
208
82

abbreviated as P b, P b, and P b.
206 207 208

 Exercise 1.1.1

Identify the element with 35 protons and write the symbols for its isotopes with 44 and 46 neutrons.

Answer
79
35
Br and 81
35
Br or, more commonly, 79
Br and 81
Br .

Summary
The atom consists of discrete particles that govern its chemical and physical behavior. Each atom of an element contains the same
number of protons, which is the atomic number (Z). Neutral atoms have the same number of electrons and protons. Atoms of an
element that contain different numbers of neutrons are called isotopes. Each isotope of a given element has the same atomic
number but a different mass number (A), which is the sum of the numbers of protons and neutrons. The relative masses of atoms
are reported using the atomic mass unit (amu), which is defined as one-twelfth of the mass of one atom of carbon-12, with 6
protons, 6 neutrons, and 6 electrons.

1.1: Atomic Structure - The Nucleus is shared under a CC BY-SA 4.0 license and was authored, remixed, and/or curated by Steven Farmer,
Dietmar Kennepohl, Tim Soderberg, William Reusch, & William Reusch.

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1.2: 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).

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 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.

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 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.

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 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.

1.2: Atomic Structure - Orbitals is shared under a CC BY-NC-SA 3.0 license and was authored, remixed, and/or curated by Steven Farmer &
Dietmar Kennepohl.

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1.3: 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 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
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.
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 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.

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 Figure 1.3.1 The Periodic Table
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

Pauli Exclusion Principle
The Pauli exclusion principle states that no two electrons can have the same four quantum numbers. The first three (n, l, and ml)
may be the same, but the fourth quantum number must be different. A single orbital can hold a maximum of two electrons, which
must have opposing spins; otherwise they would have the same four quantum numbers, which is forbidden. One electron is spin up
(ms = +1/2) and the other would spin down (ms = -1/2). This tells us that each subshell has double the electrons per orbital. The s
subshell has 1 orbital that can hold up to 2 electrons, the p subshell has 3 orbitals that can hold up to 6 electrons, the d subshell has
5 orbitals that hold up to 10 electrons, and the f subshell has 7 orbitals with 14 electrons.

 Example 1: Hydrogen and Helium

The first three quantum numbers of an electron are n=1, l=0, ml=0. Only two electrons can correspond to these, which would
be either ms = -1/2 or ms = +1/2. As we already know from our studies of quantum numbers and electron orbitals, we can
conclude that these four quantum numbers refer to the 1s subshell. If only one of the ms values are given then we would have
1s1 (denoting hydrogen) if both are given we would have 1s2 (denoting helium). Visually, this is be represented as:

As shown, the 1s subshell can hold only two electrons and, when filled, the electrons have opposite spins.

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Hund's Rule
When assigning electrons in orbitals, each electron will first fill all the orbitals with similar energy (also referred to as degenerate)
before pairing with another electron in a half-filled orbital. Atoms at ground states tend to have as many unpaired electrons as
possible. When visualizing this processes, think about how electrons are exhibiting the same behavior as the same poles on a
magnet would if they came into contact; as the negatively charged electrons fill orbitals they first try to get as far as possible from
each other before having to pair up.

 Example 2: Oxygen and Nitrogen

If we look at the correct electron configuration of the Nitrogen (Z = 7) atom, a very important element in the biology of plants:
1s2 2s2 2p3

We can clearly see that p orbitals are half-filled as there are three electrons and three p orbitals. This is because Hund's Rule
states that the three electrons in the 2p subshell will fill all the empty orbitals first before filling orbitals with electrons in them.
If we look at the element after nitrogen in the same period, oxygen (Z = 8) its electron configuration is: 1s2 2s2 2p4 (for an
atom).

Oxygen has one more electron than nitrogen and as the orbitals are all half filled the electron must pair up.

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 1.3.2

Figure 1.3.2 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
The general order in which orbitals are filled is depicted in Figure 1.3.3. 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

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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 1.3.3 : 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 Aufbau Process

Aufbau comes from the German word "aufbauen" meaning "to build." When writing electron configurations, orbitals are built up
from atom to atom. When writing the electron configuration for an atom, orbitals are filled in order of increasing atomic number.
However, there are some exceptions to this rule.

 Example 3: 3rd row elements

Following the pattern across a period from B (Z=5) to Ne (Z=10), the number of electrons increases and the subshells are
filled. This example focuses on the p subshell, which fills from boron to neon.
B (Z=5) configuration: 1s2 2s2 2p1
C (Z=6) configuration:1s2 2s2 2p2
N (Z=7) configuration:1s2 2s2 2p3
O (Z=8) configuration:1s2 2s2 2p4
F (Z=9) configuration:1s2 2s2 2p5
Ne (Z=10) configuration:1s2 2s2 2p6

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.
Table 1.3.1 Valence electrons derived from periodic table group
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

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 Periodic table group Valence electrons

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.
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.

 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:

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.

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  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 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.
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.

1.3: Atomic Structure - Electron Configurations is shared under a CC BY-SA 4.0 license and was authored, remixed, and/or curated by Steven
Farmer, Dietmar Kennepohl, Tim Soderberg, & Tim Soderberg.

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1.4: 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.

 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
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.
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.

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 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:

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

Figure 1.4.2 : Lewis Dot Symbols for the Elements in Period 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. Lewis
symbols are a tool to help draw structures. We will see why bonding in molecular compounds follow Lewis' theory in the next
section.
Elements in the same group have the same number of valence electrons and similar Lewis symbols. For example, the electron
configuration for atomic sulfur is [Ne]3s23p4, thus there are six valence electrons. Its Lewis symbol would therefore be similar to
oxygen and look like:

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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's idea of an octet explains why noble gases rarely form compounds. They have the stable s2p6 configuration (full octet, no
charge), so they have no reason to react and change their configuration. All other elements attempt to gain, lose, or share electrons
to achieve a noble gas configuration. This explains why atom combine together to form compounds. By forming bond the makes
the atoms more stable and lower in energy. Making bonds releases energy and represents a driving force for the formation of
compounds.
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.

Lewis Structures
Lewis structures represent how Lewis symbols gain, lose, or share electrons to obtain an octet by forming compounds.

Lewis Structures of Ionic Compounds

Whenever there is a metal present in the structure of an organic compound, there is a high likelihood that at least one ionic bond is
present. Ionic bonds are represented differently in Lewis structures than covalent bonds. Great care should be taken whenever
drawing the Lewis structure of an organic compounds which contains and ionic bond. Ionic bonds typically are formed when a
metal and a nonmetal are part of a compound. Some atoms achieve an octet by fully gaining or losing electrons to form ions. Ionic
bonds form through the eletrostatic attraction of the created ions. The formula for table salt is NaCl. It is the result of Na+ ions and
Cl- ions bonding together. If sodium metal and chlorine gas mix under the right conditions, they will form salt. The sodium loses an
electron, and the chlorine gains that electron. In the process, a great amount of light and heat is released. The resulting salt is
mostly unreactive — it is stable. It will not undergo any explosive reactions, unlike the sodium and chlorine that it is made of.
Why? Referring to the octet rule, atoms attempt to get a noble gas electron configuration, which is eight valence electrons. Sodium
(1s22s22p63s1) has one valence electron, so giving it up would result in the same electron configuration as neon (1s22s22p6).
Chlorine (1s22s22p63s23p7)has seven valence electrons, so if it takes one it will have eight (an octet). Chlorine has the electron
configuration of argon (1s22s22p63s23p8) when it gains an electron.
The Lewis structure of an ionic compound show the movement of electrons. For NaCl, sodium is in group 1 and has one valence
electron and chlorine is in group 17 and has seven valence electrons. Sodium loses its sole valence electron thereby becomes
positively charged. Chlorine gains this electron, gaining a full octet, and a negative charge. After the gain/loss of an electron the
new Lewis structures of Na+ and Cl- are written next to each other representing the ionic bond in NaCl.
Examples of Lewis Structures of Ionic Compounds

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Covalent Bonds and the Lewis Structures of Molecular Compounds
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 octet by sharing electrons with other atoms, forming 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 structure of H2, each pair of electrons that is shared between
two atoms is drawn as a single line, designating a single covalent bond.
H H H H or H H
two hydrogen atoms a hydrogen molecule (H2)

Hydrogen represents a special case, because a hydrogen atom cannot fulfill the octet rule; it needs only two electrons to have a full
shell. This is often called 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
a Lewis structure, we first must recognize that, although a carbon atom has a total of six electrons it's Lewis symbol has four
unpaired electrons. Following Lewis' theory the carbon atom wants to form four covalent bonds to fill its octet. 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).
H H
H
H C H H C H or H C H
H H
H

The next relatively simple organic molecule to consider is ethane, which has the molecular formula C2H6. If we draw each atom's
Lewis symbol 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.
H H H H
H H
H C C H H C C H or H C C H
H H H H
H H

The same approach can be used for molecules in which there is no carbon atom. In a water molecule, the Lewis symbol of the
oxygen atom has two unpaired electrons. These are paired with the single electron in the Lewis symbols of the hydrogens' two O-H
covalent bonds. The remaining four non-bonding electrons on oxygen called ‘lone pairs’.

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 H H
H
or
O H O H O H

Since the lone pair electrons are often NOT shown in chemical structures, it is important to see mentally add the lone pairs. In the
beginning, it can be helpful to physically add the lone pair electrons.
lone pair lone pairs
H H H H

H C N H H C C O H C Cl lone pairs

H H
H H H H

methylamine ethanol chloromethane

Exercise
For the following structure, please fill in all of the missing lone pair electrons.

Answer

When two or more electrons are shared between atoms a multiple covalent bond is formed. 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 Lewis symbols of the
atoms, 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. Ethene contains a carbon/carbon double bond.
H H H H
H H
H C C H H C C H or H C C H

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.

H C C H H C C H or H C C H

 Exercise 1.4.1

Draw the Lewis structure for ammonia, NH3.

Answer

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.)

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 H in-plane bond
C H dashed bond
H H wedged bond

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.

H H H
C H N H O
H H H
H
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 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

H Be H or H Be H
Figure 1.4.4: Lewis Structure for BeH2

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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

O C O

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

Cl
B
Cl Cl

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

2−
O
C
O O

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.

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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.

S
O O

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 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°).

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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
H
H C H
H
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

H N H
H
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.
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

H O H

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.

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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.

1.4: Development of Chemical Bonding Theory is shared under a CC BY-SA 4.0 license and was authored, remixed, and/or curated by Steven
Farmer & Krista Cunningham.

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1.5: Describing 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. 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
bond length
sigma (σ) bond
pi (π) bond
valence bond theory

Valence Bond Theory

As we have been discussing how to use Lewis structures to depict the bonding in organic compounds, we have been very vague so
far in our language about the actual nature of the chemical bonds themselves. We know that a covalent bond involves the ‘sharing’
of a pair of electrons between two atoms – but how does this happen, and how does it lead to the formation of a bond holding the
two atoms together? Two main models have been developed to described how covalent bonds are formed: valence bond theory and
molecularly orbital theory.
Valence bond theory is most often used to describe bonding in organic molecules. In this model, covalent bonds are considered to
form from the overlap of two atomic orbitals on different atoms, each orbital containing a single electron. The electrons become
paired in the orbital overlap bonding the atoms together.
The simplest example valence bond theory can be demonstrated by the H2 molecule. We can see from the periodic table that each
hydrogen atom has a single valence 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 the noble gas helium and is more stable. The 2 electrons shared in
the orbital overlap are represented by 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 which contains two electrons of opposite spin. The mutual attraction between this negatively charged electron pair and the
two atoms’ positively charged nuclei serves to physically link the two atoms through a force we define as a covalent bond. The
strength of a covalent bond depends on the extent of overlap of the orbitals involved. Orbitals that overlap extensively form bonds
that are stronger than those that have less overlap.

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ne more characteristic of the covalent bond in H2 is important to consider at this point. The two overlapping 1s orbitals can be
visualized as two spherical balloons being pressed together. This means that the bond has cylindrical symmetry: if we were to take
a cross-sectional plane of the bond at any point, it would form a circle. This type of bond is referred to as a σ(sigma) bond.

The energy of the system depends on how much the orbitals overlap. The energy diagram below illustrates how the sum of the
energies of two hydrogen atoms (the colored curve) changes as they approach each other. When the atoms are far apart there is no
overlap, and by convention we set the sum of the energies at zero. As the atoms move together, their orbitals begin to overlap. Each
electron begins to feel the attraction of the nucleus in the other atom. In addition, the electrons begin to repel each other, as do the
nuclei. While the atoms are still widely separated, the attractions are slightly stronger than the repulsions, and the energy of the
system decreases. (A bond begins to form.) As the atoms move closer together, the overlap increases, so the attraction of the nuclei
for the electrons continues to increase (as do the repulsions among electrons and between the nuclei). At some specific distance
between the atoms, which varies depending on the atoms involved, the energy reaches its lowest (most stable) value. This optimum
distance between the two bonded nuclei is called the the bond lengths between the two atoms. The bond is stable because at this
point, the attractive and repulsive forces combine to create the lowest possible energy configuration.

Figure 1.5.2 A Plot of Potential Energy versus Internuclear Distance for the Interaction between Two Gaseous Hydrogen Atoms
This optimal internuclear distance is the bond length. For the H2 molecule, the distance is 74 pm (picometers, 10-12 meters).
Likewise, the difference in potential energy between the lowest energy state (at the optimal internuclear distance) and the state

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where the two atoms are completely separated is called the bond dissociation energy, or, more simply, bond strength. For the
hydrogen molecule, the H-H bond strength is equal to about 435 kJ/mol. This means it would take 435 kJ to break one mole of H-H
bonds.
Every covalent bond in a given molecule has a characteristic length and strength. In general, the length of a typical carbon-carbon
single bond in an organic molecule is about 150 pm, while carbon-carbon double bonds are about 130 pm, carbon-oxygen double
bonds are about 120 pm, and carbon-hydrogen bonds are in the range of 100 to 110 pm. The strength of covalent bonds in organic
molecules ranges from about 234 kJ/mol for a carbon-iodine bond (in thyroid hormone, for example), about 410 kJ/mole for a
typical carbon-hydrogen bond, and up to over 800 kJ/mole for a carbon-carbon triple bond.

Representative Bond Energies and Lengths

Bond Length (pm) Energy (kJ/mol) Bond Length (pm) Energy (kJ/mol)

H-H 74 436 C-O 140.1 358

H-C 106.8 413 C=O 119.7 745

H-N 101.5 391 C≡O 113.7 1072

H-O 97.5 467 H-Cl 127.5 431

C-C 150.6 347 H-Br 141.4 366

C=C 133.5 614 H-I 160.9 298

C≡C 120.8 839 O-O 148 146

C-N 142.1 305 O=O 120.8 498

C=N 130.0 615 F-F 141.2 159

C≡N 116.1 891 Cl-Cl 198.8 243

Exercises
1) For the following energy diagram for energy vs. intermolecular distance is for a fluorine molecule (F2). Please describe the
importance for points A, B, & C on the graph.

Solutions
1)
A - Repulsive Forces are present, nuclei are too close to one another.
B - Optimal distance between the two orbitals to have a bond (the bond length)
C - Cannot form a bond, the orbitals are too far apart.

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.

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Solutions
S1.5.1

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 and Attributions

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

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/85abf193-
[email protected]).

1.5: Describing Chemical Bonds - Valence Bond Theory is shared under a CC BY-SA 4.0 license and was authored, remixed, and/or curated by
Steven Farmer & Dietmar Kennepohl.

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1.6: 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°.

Valence Bond Theory

Valence bond theory's use of overlapping atomic orbitals to explain how chemical bonds form works well in simple diatomic
molecules such as H2. However, when molecules with more than two atoms form stable bonds, we require a more detailed model.
A good example is methane (CH4). According to valence bond theory, the structure of a covalent species can be depicted using a
Lewis structure.
H
H C H
H
1

Experimentally, it has been shown that the four carbon-hydrogen bonds in the methane molecule are identical, meaning they have
the same bond energy and the same bond length. Also, VSEPR theory suggests that the geometry at the carbon atom in the methane
molecule is tetrahedral (2), and there exists a large body of both theoretical and experimental evidence supporting this prediction.
H
C H
H H

According to valence bond theory, to form a covalent bond forms when an unpaired electron in one atom overlaps with an unpaired
electron in a different atom. Now, consider the the electron configuration of the four valence electrons in carbon.

2s 2p x 2p y 2p z

There is a serious mismatch between the electron configuration of carbon (1s22s22p2) and the predicted structure of methane. The
modern structure shows that there are only 2 unpaired electrons to share with hydrogens, instead of the 4 needed to create methane.
Also, the px and py orbitals are at 90o to each other. They would form perpendicular bonds instead of the tetrahedral 109.5o bond
angle predicted by VSEPR and experimental data. Lastly, there are two different orbitals, 2s and 2p, which would create different
types of C-H bonds. As noted earlier, experimentally, the four carbon-hydrogen bonds in the methane molecule are identical.

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Hybrid Orbitals
An answer to the problems posed above was offered in 1931 by Linus Pauling. He showed mathematically that an s orbital and
three p orbitals on an atom can combine to form four equivalent hybrid atomic orbitals.

 Important Ideals in Understanding Hybridization

1. Hybrid orbitals do not exist in isolated atoms. They are formed only in covalently bonded atoms.
2. Hybrid orbitals have shapes and orientations that are very different from those of the atomic orbitals in isolated atoms.
3. A set of hybrid orbitals is generated by combining atomic orbitals. The number of hybrid orbitals in a set is equal to the
number of atomic orbitals that were combined to produce the set.
4. All orbitals in a set of hybrid orbitals are equivalent in shape and energy.
5. The type of hybrid orbitals formed in a bonded atom create the molecular geometry as predicted by the VSEPR theory.
6. Hybrid orbitals overlap to form σ bonds.
7. Lone pair electrons are often contained in hybrid orbitals

sp3 Hybridization in Methane

In order to explain this observation, valence bond theory relies on a concept called orbital hybridization. In this picture, the four
valence orbitals of the carbon (one 2s and three 2p orbitals) combine mathematically (remember: orbitals are described by
equations) to form four equivalent hybrid orbitals, which are named sp3 orbitals because they are formed from mixing one s and
three p orbitals. In the new electron configuration, each of the four valence electrons on the carbon occupies a single sp3 orbital
creating four unpaired electrons.

2s 2p x 2p y 2p z sp 3

The shape of an sp3 hybridized orbital is a combination of s and p atomic orbitals.

Each sp3-hybridized orbital bears an electron, and electrons repel each other. To minimize the repulsion between electrons, the four
sp3-hybridized orbitals arrange themselves around the carbon nucleus so that they are as far away as possible from each other,
resulting in the tetrahedral arrangement predicted by VSPER. The carbon atom in methane is called an “sp3-hybridized carbon
atom.” The larger lobes of the sp3 hybrids are directed towards the four corners of a tetrahedron, meaning that the angle between
any two orbitals is 109.5o.

Bonding in Methane
Each C-H bond in methane, then, can be described as an overlap between a half-filled 1s orbital in four hydrogen atoms and the
larger lobe of one of the four half-filled sp3 hybrid orbitals form a four equivalent sigma (σ) bond. This orbital overlap is often
described using the notation: sp3(C)-1s(H). The formation of sp3 hybrid orbitals successfully explains the tetrahedral structure of
methane and the equivalency of the the four C-H bonds.
What remains is an explanation of why the sp3 hybrid orbitals form. When the s and 3 p orbitals in carbon hybridize the resulting
sp3 hybrid orbital is unsymmetrical with one lobe larger than the other. This means the larger lobe can overlap more effectively

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with orbitals from other bonds making them stronger. Hybridizing allows for the carbon to form stronger bonds than it would with
unhybridized s or p orbitals.

The four carbon-hydrogen bonds in methane are equivalent and all have a bond length of 109 pm (1.09 x 10-10 m), bond strength
of of 429 kJ/mol. All of the H-C-H bond angles are 109.5o.

H
bond angle (109.5°) bond length (109 pm)
C H
H H

 Looking Closer: Linus Pauling

Arguably the most influential chemist of the 20th century, Linus Pauling (1901–1994) is the only person to have won two
individual (that is, unshared) Nobel Prizes. In the 1930s, Pauling used new mathematical theories to enunciate some
fundamental principles of the chemical bond. His 1939 book The Nature of the Chemical Bond is one of the most significant
books ever published in chemistry.
Pauling's big contribution to chemistry was valence bond theory, which combined his knowledge of quantum mechanical
theory with his knowledge of basic chemical facts, like bond lengths and and bond strengths and shapes of molecules. Valence
bond theory, like Lewis's bonding theory, provides a simple model that is useful for predicting and understanding the structures
of molecules, especially for organic chemistry. .
By 1935, Pauling’s interest turned to biological molecules, and he was awarded the 1954 Nobel Prize in Chemistry for his
work on protein structure. (He was very close to discovering the double helix structure of DNA when James Watson and James
Crick announced their own discovery of its structure in 1953.) He was later awarded the 1962 Nobel Peace Prize for his efforts
to ban the testing of nuclear weapons.

Linus Pauling was one of the most influential chemists of the 20th century.

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 In his later years, Pauling became convinced that large doses of vitamin C would prevent disease, including the common cold.
Most clinical research failed to show a connection, but Pauling continued to take large doses daily. He died in 1994, having
spent a lifetime establishing a scientific legacy that few will ever equal

1.6: sp³ Hybrid Orbitals and the Structure of Methane is shared under a CC BY-SA 4.0 license and was authored, remixed, and/or curated by
Steven Farmer, Dietmar Kennepohl, Krista Cunningham, Tim Soderberg, Gamini Gunawardena, & Gamini Gunawardena.

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1.7: 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.

Bonding in Ethane
H H H H
H H CH3CH3 H
H
H H H H

Representations of Ethane
The simplest molecule with a carbon-carbon bond is ethane, C2H6. In ethane (CH3CH3), both carbons are sp3-hybridized, meaning
that both have four bonds with tetrahedral geometry. An sp3 orbital of one carbon atom overlaps end to end with an sp3 orbital of
the second carbon atom to form a carbon-carbon σ bond. This orbital overlap is often described using the notation: sp3(C)-sp3(C).
Each of the remaining sp3 hybrid orbitals overlaps with the s orbital of a hydrogen atom to form carbon–hydrogen σ bonds.

H H
H H
C C
H H H H
H H H H

The σ carbon-carbon bond has a bond length of 154 pm, and a bond strength of 377 kJ/mol. The carbon-hydrogen σ bonds are
slightly weaker, 421 kJ/mol, than those of methane. The C-C-H bond angles in ethane are 111.2o which is close to the what is
expected for tetrahedral molecules.

H 111.2° H
C C
H H
H 154 pm H
The orientation of the two CH3 groups is not fixed relative to each other. 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 Section 3.7 we will learn more about the
implications of rotational freedom in sigma bonds, when we discuss the ‘conformation’ of organic molecules
free rotation

Ha Ha Ha Hc
Hb
C C C C
Hb Hb Hb
Hc Hc Hc Ha

 How did they know?

The tetrahedral geometry of carbon was predicted as far back as 1874. But how did they know? A question came up when
looking at ethane with a bromine substituent (C2H5Br). When looking at the possible structures of the compound C2H5Br there
are several possible structural formulas.here was a serious problem as to whether these formulas represent the same or different
compounds. All that was known in the early days was that every purified sample of C2H5Br, no matter how prepared, had a
boiling point of 38 oC and density of 1.460 gml−1. Furthermore, all looked the same, all smelled the same, and all underwent

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 the same chemical reactions. There was no evidence that C2H5Br was a mixture or that more than one compound of this
formula could be prepared. One might conclude, therefore, that all of the structural formulas above represent a single substance
but how? A brilliant solution to the problem came when J. H. van 't Hoff proposed that all four bonds of carbon are equivalent
and directed to the corners of a regular tetrahedron. If we redraw the structures for C2H5Br with both carbons having
tetrahedral geometry, we see that there is only one possible arrangement. This theory hints at the idea of free rotation around
sigma bonds which will be discussed later.

There was a serious problem as to whether these formulas represent the same or different compounds. All that was known in
the early days was that every purified sample of C2H5Br, no matter how prepared, had a boiling point of 38 oC and density of
1.460 gml−1. Furthermore, all looked the same, all smelled the same, and all underwent the same chemical reactions. There was
no evidence that C2H5Br was a mixture or that more than one compound of this formula could be prepared. One might
conclude, therefore, that all of the structural formulas above represent a single substance but how? A brilliant solution to the
problem came when J. H. van 't Hoff proposed that all four bonds of carbon are equivalent and directed to the corners of a
regular tetrahedron. If we redraw the structures for C2H5Br with both carbons having tetrahedral geometry, we see that there is
only one possible arrangement. This theory hints at the idea of free rotation around sigma bonds which will be discussed later.

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.

1.7: sp³ Hybrid Orbitals and the Structure of Ethane is shared under a CC BY-SA 4.0 license and was authored, remixed, and/or curated by Steven
Farmer, Dietmar Kennepohl, Krista Cunningham, Tim Soderberg, William Reusch, & William Reusch.

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1.8: 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
Thus far valence bond theory has been able to describe the bonding in molecules containing only single bonds. However, when
molecules contain double or triple bonds the model requires more details. Ethylene (commonly knows as ethene), CH2CH2, is the
simplest molecule which contains a carbon carbon double bond. The Lewis structure of ethylene indicates that there are one
carbon-carbon double bond and four carbon-hydrogen single bonds. Experimentally, the four carbon-hydrogen bonds in the
ethylene molecule have been shown to be identical. Because each carbon is surrounded by three electron groups, VSEPR theory
says the molecule should have a trigonal planar geometry. Although each carbon has fulfilled its tetravalent requirement, one bond
appears different. Clearly, a different type of orbital overlap is involved.

H H
C C
H H
The sigma bonds formed in ethene is by the participation of a different kind of hybrid orbital. Three atomic orbitals on each carbon
– the 2s, 2px and 2py – combine to form three sp2 hybrids, leaving the 2pz orbital unhybridized. Three of the four valence electrons
on each carbon are distributed to the three sp2 hybrid orbitals, while the remaining electron goes into the unhybridized pz orbital.
Each carbon in ethene is said to be a “sp2-hybridized carbon.” The electron configuration of the sp2 hybridized carbon shows that
there are four unpaired electrons to form bonds. However, the unpaired electrons are contained in two different types of orbitals so
it is to be expected that two different types of bonds will form.

2s 2p x 2p y 2p z sp 2 2p z

The shape of the sp2-hybridized orbital has be mathematically shown to to be roughly the same as that of the sp3-hybridized orbital.
To minimize the repulsion between electrons, the three sp2-hybridized orbitals are arranged with a trigonal planar geometry. Each
orbital lobe is pointing to the three corners of an equilateral triangle, with angles of 120° between them. Again, geometry and
hybrization can be tied together. Atoms surrounded by three electron groups can be said to have a trigonal planar geometry and sp2
hybridization.

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The unhybridized 2pz orbital is perpendicular to the plane of the trigonal planar sp2 hybrid orbtals.

In the ethylene molecule, each carbon atom is bonded to two hydrogen atoms. Thus, overlap two sp2-hybridized orbitals with the 1s
orbitals of two hydrogen atoms for the C-H sigma bonds in ethylene (sp2(C)-1s(H). Consequently, consistent with the observations,
the four carbon-hydrogen bonds in ethylene are identical.

The C-C sigma bond in ethylene is formed by the overlap of an sp2 hybrid orbital from each carbon.

The overlap of hybrid orbitals or a hybrid orbital and a 1s orbtial from hydrogen creates the sigma bond framework of the ethylene
molecule. However the unhybridized pz orbital on each carbon remains.

The unhybridized pz orbitals on each carbon overlap to a π bond (pi). The orbital overlap is commonly written as pz(C)-1pz(C). In
general multiple bonds in molecular compound are formed by the overlap of unhybridized p orbitals. It should be noted that the
carbon-carbon double bond in ethlene is made up of two different types of bond, a sigma and a pi.

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Overall, ethylene is said to contain five sigma bonds and one pi bond. Pi bonds tend to be weaker than sigma bonds because the
side-by-side overlap the p orbitals give a less effective orbital overlap when compared to the end-to-end orbital overlap of a sigma
bond. This makes the pi much easier to break which is one of the most important ideas in organic chemistry reactions as we will
see in Chapter 7 and subsequent chapters.
pi bond
H H
C C
H H
sigma bonds

An ethylene molecule is said to be made up of five sigma bonds and one pi bond. The three sp2 hybrid orbitals on each carbon
orient to create the basic trigonal planer geometry. The H-C-C bond angle in ethylene is 121.3o which is very close to the 120o
predicted by VSEPR. The four C-H sigma bonds in ethylene . The carbon-carbon double bond in ethylene is both shorter (133.9
pm) and almost twice as strong (728 kJ/mol) than the carbon- carbon single bond in ethylene (154 pm & 377 kJ/mol). Each of the
four carbon-hydrogen bond in ethylene are equivalent has have a length of 108.7 pm

H 121.3° H
C C 108.7 pm

H H
133.9 pm

Rigidity in Ethene
Because they are the result of side-by-side overlap (rather then end-to-end overlap like a sigma bond), pi bonds are not free to
rotate. If rotation about this bond were to occur, it would involve disrupting the side-by-side overlap between the two 2pz orbitals
that make up the pi bond. If free rotation were to occur the p-orbitals would have to go through a phase where they are 90° from
each other, which would break the pi bond because there would be no overlap. Since the pi bond is essential to the structure of
ethene it must not break, so there can be not free rotation about the carbon-carbon sigma bond. The presence of the pi bond thus
‘locks’ the six atoms of ethene into the same plane.

Exercise
1) Consider the following molecule:

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At each atom, what is the hybridization and the bond angle and the bond angle predicted by VSPER?
2) Please identify the types of orbitals shown in the following diagram:

3)
a: Describe the orbitals which overlap to the carbon-nitrogen sigma bond and pie bond in the molecule below:

b: What kind of orbital holds the nitrogen lone pair?

4) For the following molecule please indicate with atoms are being held in the same plane by the carbon-carbon double bond:

Solutions
1)
A - sp2, 120°
B - sp3, 109°
C - sp2, 120° (with the lone pairs present)
D - sp3, 109°
2)

3)
a) The carbon and nitrogen atoms are both sp2 hybridized. The carbon-nitrogen double bond is composed of a sigma bond formed
from two sp2 orbitals, and a pi bond formed from the side-by-side overlap of two unhybridized 2p orbitals.

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b) As shown in the figure above, the nitrogen lone pair electrons occupy one of the three sp2 hybrid orbitals.
4)

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°

1.8: sp² Hybrid Orbitals and the Structure of Ethylene is shared under a CC BY-SA 4.0 license and was authored, remixed, and/or curated by
Steven Farmer, Dietmar Kennepohl, Krista Cunningham, Tim Soderberg, William Reusch, & William Reusch.

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1.9: 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.

H C C H
ethyne
(acetylene)
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.

2s 2p x 2p y 2p z sp 2p y 2p z

2p y
(perpendicular to the
2p z plane of the page)

sp C sp

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

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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).

H C C H
H C C H

sigma bonding in ethylene pi bonding in ethylene

Acetylene is said to have three sigma bonds and two pi bonds. The carbon-carbon triple bond in acetylene is the shortest (120 pm)
and the strongest (965 kJ/mol) of the carbon-carbon bond types. Because each carbon in acetylene has two electron groups, VSEPR
predicts a linear geometry and and H-C-C bond angle of 180o.
106 pm
180°

H C C H

120 pm

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, HC≡CH (sp) C≡C (sp) 965 120

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

sp 3-sp 3 sp 2-sp 3
sp -sp 3
H H
H CH3
H C C H C C H C C CH3
H H H H

A B C

In propene (B), however, the carbon-carbon single bond is the result of overlap between an sp2 orbital and an sp3 orbital, while in
propyne (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.

Hybridization Summary
A single bond is a sigma bond.
A double bond is made up of a sigma bond and a pi bond.
A triple bond is made up of a sigma bond and two pi bonds.
Sigma bonds are made by the overlap of two hybrid orbitals or the overlap of a hybrid orbital and a s orbital from hydrogen.
Pi bonds are made by the overlap of two unhybridized p orbitals.

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 Lone pair electrons are usually contained in hybrid orbitals.
The hybrid orbitals used (and hence the hybridization) depends on how many electron groups are around the atom in question. An
electron group can mean either a bonded atom or a lone pair. Molecular geometry is also decided by the number of electron groups
so it is directly linked to hybridization.

# of Electron Groups Hybrid Orbital Used Example Basic Geometry Basic Bond Angle

2 sp C Linear 180o

3 sp2 C Trigonal Planar 120o

4 sp3 C Tetrahedral 109.5o

Exercises
1) For the molecule acetonitrile:

a) How many sigma and pi bonds does it have?

b) What orbitals overlap to form the C-H sigma bonds?
c) What orbitals overlap to form the C-C sigma bond?
d) What orbitals overlap to form the C-N sigma bond?
e) What orbitals overlap to the form the C-N pi bonds?
f) What orbital contains the lone pair electrons on nitrogen?

Solutions
1)
a) 5 sigma and 2 pi
b) An sp3 hybrid orbital from carbon and an a s orbital from hydrogen.
c) An sp3 hybrid orbital from one carbon and an a sp3 orbital from the other carbon.
d) An sp hybrid orbital from carbon and an a sp orbital from nitrogen.
e) An py and pz orbital from carbon and an py and pz orbital from nitrogen.
f) An sp hybrid orbital.
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.

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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°.

1.9: sp Hybrid Orbitals and the Structure of Acetylene is shared under a CC BY-SA 4.0 license and was authored, remixed, and/or curated by
Steven Farmer, Dietmar Kennepohl, Krista Cunningham, Tim Soderberg, William Reusch, & William Reusch.

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1.10: 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.

Nitrogen
Bonding in NH3
The nitrogen in NH3 has five valence electrons. After hybridization these five electrons are placed in the four equivalent sp3 hybrid
orbitals. The electron configuration of nitrogen now has one sp3 hybrid orbital completely filled with two electrons and three sp3
hybrid orbitals with one unpaired electron each. The two electrons in the filled sp3 hybrid orbital are considered non-bonding
because they are already paired. These electrons will be represented as a lone pair on the structure of NH3. The three unpaired
electrons in the hybrid orbitals are considered bonding and will overlap with the s orbitals in hydrogen to form N-H sigma bonds.
Note! This bonding configuration was predicted by the Lewis structure of NH3.
lone pair bonding electrons
electrons

nitrogen

2s 2p x 2p y 2p z four sp 3 hybrid orbitals

The four sp3 hybrid orbitals of nitrogen orientate themselves to form a tetrahedral geometry. The three N-H sigma bonds of NH3
are formed by sp3(N)-1s(H) orbital overlap. The fourth sp3 hybrid orbital contains the two electrons of the lone pair and is not
directly involved in bonding.

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.

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 H

N H N C H
H CH3 H H
H
sp 3(N)-sp 3(C) overlap
forms a sigma bond

Oxygen
Bonding in H2O
The oxygen in H2O has six valence electrons. After hybridization these six electrons are placed in the four equivalent sp3 hybrid
orbitals. The electron configuration of oxygen now has two sp3 hybrid orbitals completely filled with two electrons and two sp3
hybrid orbitals with one unpaired electron each. The filled sp3 hybrid orbitals are considered non-bonding because they are already
paired. These electrons will be represented as a two sets of lone pair on the structure of H2O . The two unpaired electrons in the
hybrid orbitals are considered bonding and will overlap with the s orbitals in hydrogen to form O-H sigma bonds. Note! This
bonding configuration was predicted by the Lewis structure of H2O.
lone pair bonding electrons
electrons

oxygen

2s 2p x 2p y 2p z four sp 3 hybrid orbitals

The four sp3 hybrid orbitals of oxygen orientate themselves to form a tetrahedral geometry. The two O-H sigma bonds of H2O are
formed by sp3(O)-1s(H) orbital overlap. The two remaining sp3 hybrid orbitals each contain two electrons in the form of a lone
pair.

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.

H
O C
O H
H CH3 H H

sp 3(O)-sp 3(C) overlap

forms a sigma bond

Phosphorus
Methyl phosphate
The bond pattern of phosphorus is analogous to nitrogen because they are both in period 15. However, 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.

1.10.2 https://chem.libretexts.org/@go/page/31377
 ~110°O
O P CH3
O O

Sulfur
Methanethiol & Dimethyl Sulfide
Sulfur has a bonding pattern similar to oxygen because they are both in period 16 of the periodic table. Because sulfur is positioned
in the third row of the periodic table it has the ability to form an expanded octet and the ability to form more than the typical
number of covalent bonds. 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. The simplest example of a thiol is methane thiol (CH3SH) and the simplest example of a sulfide is dimethyl sulfide
[(CH3)3S]. In both cases the sulfur is sp3 hybridized, however the sulfur bond angles are much less than the typical tetrahedral
109.5o being 96.6o and 99.1o respectively.

H
S
H CH3 S C
H
H 96.5° H

methanethiol

H
S
H3 C CH3 S C
H
H3 C 99.1° H

dimethyl sulfide

Exercises
1) Insert
the missing lone pairs of electrons in the following molecules, and tell what hybridization you
expect for each of the indicated atoms.
a) The oxygen is dimethyl ether:

O
H3C CH3
b) The nitrogen in dimethyl amine:

c) The phosphorus in phosphine:

d) The sulfur in hydrogen sulfide:

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Solutions
1)
a) sp3 hybridization

b) sp3 hybridization

c) sp3 hybridization

d) sp3 hybridization

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.

1.10: Hybridization of Nitrogen, Oxygen, Phosphorus and Sulfur is shared under a CC BY-SA 4.0 license and was authored, remixed, and/or
curated by Steven Farmer, Dietmar Kennepohl, Krista Cunningham, & Krista Cunningham.

1.10.4 https://chem.libretexts.org/@go/page/31377
1.11: Describing 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.

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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
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

In p orbitals, the wave function gives rise to two lobes with opposite phases, analogous to how a two-dimensional wave has both
parts above and below the average. We indicate the phases by shading the orbital lobes different colors. When orbital lobes of the
same phase overlap, constructive wave interference increases the electron density. When regions of opposite phase overlap, the
destructive wave interference decreases electron density and creates nodes. When p orbitals overlap end to end, they create σ and
σ* orbitals. If two atoms are located along the x-axis in a Cartesian coordinate system, the two px orbitals overlap end to end and
form σpx (bonding) and σ∗px (antibonding) (read as "sigma-p-x" and "sigma-p-x star," respectively). Just as with s-orbital overlap,
the asterisk indicates the orbital with a node between the nuclei, which is a higher-energy, antibonding orbital.

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 Ψ1 orbital when the
molecule is in the ground state.

 Example 1.11.1

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

1.11.2 https://chem.libretexts.org/@go/page/31378
 Solution
Answers

1.11: Describing Chemical Bonds - Molecular Orbital Theory is shared under a CC BY-SA 4.0 license and was authored, remixed, and/or curated
by Steven Farmer, Dietmar Kennepohl, Tim Soderberg, & Tim Soderberg.

1.11.3 https://chem.libretexts.org/@go/page/31378
1.12: 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.

Through general chemistry, you may have already experienced looking at molecular structures using Lewis structures. Because
organic chemistry can involve large molecules it would be beneficial if Lewis structures could be abbreviated. The three different
ways to draw organic molecules include Kekulé Formulas, Condensed Formulas, and Skeletal structures (also called line-bond
structures or line formulas). During this course, you will view molecules written in all three forms. It will be more helpful if you
become comfortable going from one style of drawing to another, and look at drawings and understanding what they represent.
Developing the ability to convert between different types of formulas requires practice, and in most cases the aid of molecular
models. Many kinds of model kits are available to students and professional chemists, and the beginning student is encouraged to
obtain one.
Simplification of structural formulas may be achieved without any loss of the information they convey. Kekule formulas is just
organic chemistry's term for Lewis structures you have previously encountered. 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. 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.

Kekulé (a.k.a. Lewis Structures)

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. All atom labels are shown and all lone pairs
are shown.

H
H H H C H H H H O
H C C O H H H O H H C N C C O H
H H Cl C C C C H H H
H H H H

A B C

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Condensed Formula
A condensed formula is made up of the elemental symbols. 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. The order of the atoms
suggests the connectivity in the molecule. 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. Also, if more than one of the same substituent is attached to a given atom, it is show with a subscript number. An example
is CH4, which represents four hydrogens attached to the same carbon. Condensed formulas can be read from either direction and
H3C is the same as CH3, although the latter is more common.
Look at the examples below and match them with their identical molecule under the Kekulé structures and the line formulas.

CH3CH2OH ClCH2CH2CH(OCH3)CH3 CH3NHCH2COOH

A B C

Let's look closely at example B. As you go through a condensed formula, you want to focus on the carbons and other elements that
aren't hydrogen. The hydrogen's are important, but are usually there to complete octets. Also, notice the -OCH3 is in written in
parentheses which tell you that it not part of the main chain of carbons. As you read through a a condensed formula, if you reach an
atom that doesn't have a complete octet by the time you reach the next hydrogen, then it's possible that there are double or triple
bonds. In example C, the carbon is double bonded to oxygen and single bonded to another oxygen. Notice how COOH means
C(=O)-O-H instead of CH3-C-O-O-H because carbon does not have a complete octet and oxygens.

Line 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 letter "C" with lines. A carbon atom is present wherever a line intersects another line. Hydrogen atoms
are omitted but are assumed to be present to complete each of carbon's four bonds. Hydrogens that are attached to elements other
than carbon are shown. Atom labels for all other elements are shown. Lone pair electrons are usually omitted. They are assumed to
be present to complete the octet of non-carbon atoms. Line formulas help show the structure and order of the atoms in a compound.

O O
H
OH N
Cl OH

A B C

These molecules correspond to the exact same molecules depicted for Kekulé structures and condensed formulas. Notice how the
carbons are no longer drawn in and are replaced by the ends and bends of a lines. In addition, the hydrogens have been omitted, but
could be easily drawn in (see practice problems). Although we do not usually draw in the H's that are bonded to carbon, we do
draw them in if they are connected to other atoms besides carbon (example is the OH group above in example A) . This is done
because it is not always clear if the non-carbon atom is surrounded by lone pairs or hydrogens. Also in example A, notice how the
OH is drawn with a bond to the second carbon, but it does not mean that there is a third carbon at the end of that bond/ line.
Kekulé Formula Condensed Formula Line Formula
H H H H
H C C C C O H CH3(CH2)3OH OH
H H H H

H
H H O H OH
H C C C C H
CH3CH2CH(OH)CH3
H H H H

H H H
H C C C O H
H C H
(CH3)2CHCH2OH OH
H H
H

1.12.2 https://chem.libretexts.org/@go/page/31379
 H
H O H
H C C C H (CH3)3COH
H H OH
C
H H
H

H H H H
H C C O C C H CH3CH2OCH2CH3 O
H H H H

Table 1.12.1: Structural Formulas for C4H10O isomers

Example: Converting between Structural Formulas

It is helpful to convert compounds into different structural formulas (Kekule, Line, and Condensed) depending on the type of
question that is asked. Standardized exams frequently include a high percentage of condensed formulas because it is easier and
cheaper to type letters and numbers than to import figures. Initially, it can be difficult writing a Line structure directly from a
condensed formula. First, write the Kekule structure from the condensed formula and then draw the Line structure from the Kekule.
a) The condensed formula for propanal is CH3CH2CHO. Draw the Kekule structure.
The Kekule structure for propanal is shown below. Remember that every carbon will have four bonds and oxygens octet is filled
with lone pairs.
H O
H
C C
H C H
H H

The bond-line structure for propanal is shown below. First, remove hydrogens. The hydrogen attached to the aldehyde group
remains because it is part of a functional group. The remove the "C" labels from the structure and keep the lines in place. Lastly,
remove any lone pairs.
O

All three structures represent the same compound, propanal.

H O
H O
CH3CH2CHO = C C =
H C H
H
H H

b) The following is the line structure of the molecule trimethyl amine.

To convert it to a Kekule structure first identify the carbons in the molecule. The will be at the corners and ends of line without an
atom label. Trimethyl amine has three carbons. Next, add hydrogens to the carbons until four bonds are present. Each carbon in
trimethyl amine is singly bonded to nitrogen. This means each carbon will need three additional C-H bonds to create its octet.
Lastly, add lone pairs to other elements to fill their octets. The nitrogen in trimethyl amine is bonded to three carbons. This means it
will require one of lone pair electrons to complete its octet.
H
H H
C
H N H
C C
H H
H H

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Exercises
1. How many carbons are in the following drawing? How many hydrogens?

2. How many carbons are in the following drawing? How many hydrogens?

3. How many carbons are in the following drawing? How many hydrogens?

4. Look at the following molecule of vitamin A and draw in the hidden hydrogens and electron pairs.

(hint: Do all of the carbons have 4 bonds? Do all the oxygens have a full octet?)
5. Draw ClCH2CH2CH(OCH3)CH3 in Kekulé and line form.
6. Write down the molecular formula for each of the compounds shown here.

Answers:
1. Remember the octet rule and how many times carbons and hydrogens are able to bond to other atoms.

1.12.4 https://chem.libretexts.org/@go/page/31379
 2.

3.
4. Electron pairs drawn in blue and hydrogens draw in red.

5.

6.
A. C7H7N
B. C5H10
C. C5H4O
D. C5H6Br2
Questions
Q1.12.1
Below is the molecule for caffeine. Give the molecular formula for it.

Solutions
S1.12.1
C8H10O2N4

1.12: Drawing Chemical Structures is shared under a CC BY-SA 4.0 license and was authored, remixed, and/or curated by Steven Farmer,
Dietmar Kennepohl, Krista Cunningham, Tim Soderberg, William Reusch, & William Reusch.

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1.S: 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

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 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
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

Summary Problems

 Exercise 1.S. 1

The following molecule is highly reactive and contains a functional group called a ketene. For each numbered atom, list the
geometry, bond angle, hybridization, orbitals present, and orbital function. Notes: Ignore the geometry and bond angle for atom
#1. For orbitals present, list all of the orbitals at that atom. For orbital function, describe what each orbital is doing (e.g.,
participating in a sigma bond, containing lone pair electrons, etc.).
H3 C 2
3C C O1
H3 C
4

Answer
#1 - sp2 hybridization; 3 sp2 orbitals and 1 p orbital present; p orbital participates in a pi bond, 1 sp2 orbital participates in a
sigma bond, 2 sp2 orbitals contain lone pair electrons
#2 - linear; 180 degrees; sp hybridization; 2 sp orbitals and 2 p orbitals present; p orbitals participate in two pi bonds, s sp2
orbitals participate in two sigma bonds
#3 - trigonal planar; 120 degrees; sp2 hybridization; 3 sp2 orbitals and 1 p orbital present; p orbital participates in a pi bond,
3 sp2 orbitals participate in three sigma bonds
#4 - tetrahedral; 109.5 degrees; sp3 hybridization; 4 sp3 orbitals present; 4 sp3 orbitals participate in four sigma bonds

 Exercise 1.S. 2
First, add lone pair electrons and formal charges to the molecule shown below; its net charge is plus one. (The only formal
charge on a carbon atom has already been added for you.) Second, for each numbered atom, list the geometry, bond angle,
hybridization, orbitals present, and orbital function. Notes: For orbitals present, list all of the orbitals at that atom. For orbital
function, describe what each orbital is doing (e.g., participating in a sigma bond, containing lone pair electrons, etc.).
1 3
O
2
4
N
O

Answer

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 1 3
O
2
4
N
O

#1 - linear; 180 degrees; sp hybridization; 2 sp orbitals and 2 p orbitals present; p orbitals participate in two pi bonds, s sp2
orbitals participate in two sigma bonds
#2 - trigonal planar; 120 degrees; sp2 hybridization; 3 sp2 orbitals and 1 p orbital present; p orbital is empty, 3 sp2 orbitals
participate in three sigma bonds
#3 - bent; <109.5 degrees; sp3 hybridization; 4 sp3 orbitals present; 2 sp3 orbitals participate in two sigma bonds, 2 sp3
orbitals contain two lone pairs
#4 - tetrahedral; 109.5 degrees; sp3 hybridization; 4 sp3 orbitals present; 4 sp3 orbitals participate in four sigma bonds

 Exercise 1.S. 3

First, add lone pair electrons and formal charges to the molecule shown below. Second, for each numbered atom, list the
geometry, bond angle, hybridization, orbitals present, and orbital function. Third, clearly identify on the structure below sigma
bonds formed by overlap of the following orbitals: sp-sp2 (label as “a”), sp-sp3 (label as “b”), sp2-sp2 (label as “c”), sp2-sp3
(label as “d”), and sp3-sp3 (label as “e”). Notes: For orbitals present, list all of the orbitals at that atom. For orbital function,
describe what each orbital is doing (e.g., participating in a sigma bond, containing lone pair electrons, etc.). When identifying
particular types of sigma bonds, there will be more than one correct answer for some options.
1
OH

3 O

Answer
1
OH

3 O
All atoms are neutral in this molecule.
#1 - bent; <109.5 degrees; sp3 hybridization; 4 sp3 orbitals present; 2 sp3 orbitals participate in two sigma bonds, 2 sp3
orbitals contain two lone pairs
#2 - linear; 180 degrees; sp hybridization; 2 sp orbitals and 2 p orbitals present; p orbitals participate in two pi bonds, s sp2
orbitals participate in two sigma bonds
#3 - trigonal planar; 120 degrees; sp2 hybridization; 3 sp2 orbitals and 1 p orbital present; p orbital participates in a pi bond,
3 sp2 orbitals participate in three sigma bonds
OH
b

O a
d
c e

O
For a and b, these are the only bonds that are correct. For c, there are several correct options. For d, there is
one other option (from the benzene ring to the O in the five-membered ring. For e, there are several correct options.

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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.

1.S: Structure and Bonding (Summary) is shared under a not declared license and was authored, remixed, and/or curated by Kelly Matthews &
Kevin M. Shea.

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 CHAPTER OVERVIEW
2: Polar Covalent Bonds; Acids and Bases
 Chapter Objectives

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 use of electronegativity to determine bond polarity, and the application of this knowledge to determine whether a given
molecule possesses a dipole moment.
the drawing and interpretation of organic chemical structures.
the concept and determination of formal charge.
resonance and drawing of resonance forms
the Brønsted-Lowry and Lewis definitions of acids and bases, acidity constants and acid-base reactions.
intermolecular forces

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: Noncovalent Interactions Between Molecules
2.MM: Molecular Models
2.S: Polar Covalent Bonds; Acids and Bases (Summary)

2: Polar Covalent Bonds; Acids and Bases is shared under a CC BY-SA 4.0 license and was authored, remixed, and/or curated by Steven Farmer
& Dietmar Kennepohl.

1
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
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.
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. Figure 2.1.1 shows the electronegativity
values of the elements as proposed by one of the most famous chemists of the twentieth century: Linus Pauling. 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. In general, electronegativity increases from left to right across a period in the periodic table and decreases down a group.
Thus, the nonmetals, which lie in the upper right, tend to have the highest electronegativities, with fluorine the most electronegative
element of all (EN = 4.0 as previously noted). It is important to notice that the elements most important to organic chemistry,
carbon, nitrogen, and oxygen have some of the highest electronegativites in the periodic table (EN = 2.5, 3.0, 3.5 respectively).
Metals, on the left, tend to be less electronegative elements, with cesium having the lowest (EN = 0.7). Note that noble gases are
excluded from this figure because these atoms usually do not share electrons with others atoms since they have a full valence shell.

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 Electronegativity is defined as the ability of an atom in a particular molecule to attract
electrons to itself. The larger the electronegativity value, the greater the attraction.

Figure 2.1.1 : Pauling scale electronegativities of elements

Figure 2.1.2 : Visual representation of electronegativities.

Electronegativity and Bond Type

The two idealized extremes of chemical bonding: (1) ionic bonding—in which one or more electrons are transferred completely
from one atom to another, and the resulting ions are held together by purely electrostatic forces—and (2) covalent bonding, in
which electrons are shared equally between two atoms. Most compounds, however, have polar covalent bonds, which means that
electrons are shared unequally between the bonded atoms. Electronegativity determines how the shared electrons are distributed
between the two atoms in a polar covalent bond. The more strongly an atom attracts the electrons in its bonds, the larger its
electronegativity. Electrons in a polar covalent bond are shifted toward the more electronegative atom; thus, the more
electronegative atom is the one with the partial negative charge. The greater the difference in electronegativity, the more polarized
the electron distribution and the larger the partial charges of the atoms. Recall that a lowercase Greek delta ( δ ) is used to indicate
that a bonded atom possesses a partial positive charge, indicated by δ+ , or a partial negative charge, indicated by δ− , and a bond
between two atoms that possess partial charges is a polar bond.

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 Figure 2.1.3 : The Electron Distribution in a Nonpolar Covalent Bond, a Polar Covalent Bond, and an Ionic Bond Using Lewis
Electron Structures. Electron-rich (negatively charged) regions are shown in blue; electron-poor (positively charged) regions are
shown in red.
Whether a bond is ionic, nonpolar covalent, or polar covalent can be estimated by by calculating the absolute value of the
difference in electronegativity (ΔEN) of two bonded atoms. When the difference is very small or zero, the bond is covalent and
nonpolar. When it is large, the bond is polar covalent or ionic. The absolute values of the electronegativity differences between the
atoms in the bonds H–H, H–Cl, and Na–Cl are 0 (nonpolar), 0.9 (polar covalent), and 2.1 (ionic), respectively. The degree to which
electrons are shared between atoms varies from completely equal (pure covalent bonding) to not at all (ionic bonding). Figure 7.2.4
shows the relationship between electronegativity difference and bond type. This table is just a general guide, however, with many
exceptions. The best guide to the covalent or ionic character of a bond is to consider the types of atoms involved and their relative
positions in the periodic table. Bonds between two nonmetals are generally covalent; bonding between a metal and a nonmetal is
often ionic.

Figure 2.1.4 : As the electronegativity difference increases between two atoms, the bond becomes more ionic.
Some compounds contain both covalent and ionic bonds. The atoms in polyatomic ions, such as OH–, NO3−, and NH4+, are held
together by polar covalent bonds. However, these polyatomic ions form ionic compounds by combining with ions of opposite
charge. For example, potassium nitrate, KNO3, contains the K+ cation and the polyatomic NO3− anion. Thus, bonding in potassium
nitrate is ionic, resulting from the electrostatic attraction between the ions K+ and NO3−, as well as covalent between the nitrogen
and oxygen atoms in NO3−.

Example 2.1.1: Electronegativity and Bond Polarity

Bond polarities play an important role in determining the structure of proteins. Using the electronegativity values in Table A2,
arrange the following covalent bonds—all commonly found in amino acids—in order of increasing polarity. Then designate the
positive and negative atoms using the symbols δ+ and δ–:
C–H, C–N, C–O, N–H, O–H, S–H

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Solution
The polarity of these bonds increases as the absolute value of the electronegativity difference increases. The atom with the δ–
designation is the more electronegative of the two. Table 2.1.1 shows these bonds in order of increasing polarity.
Table 2.1.1 : Bond Polarity and Electronegativity Difference
Bond ΔEN Polarity
δ− δ+
C–H 0.4 C − H

δ− δ+
S–H 0.4 S − H

δ+ δ−
C–N 0.5 C − N

δ− δ+
N–H 0.9 N − H

δ+ δ−
C–O 1.0 C − O

δ− δ+
O–H 1.4 O − H

Visualizing Bonding
Calculated charge distributions in molecules can easily be visualized by using electrostatic potential maps. The color red is used to
indicate electron-rich regions of a molecule while the color blue is used to indicated electron-poor regions. An easier method for
visually representing electron displacement in a molecule uses a crossed arrow. By convention the arrow point in the direction of
the electron-rich region of a molecule and away from the electron-poor. An example is shown in the molecule fluoromethane. The
C-F bond is polarized drawing the bonding electrons toward the more electronegative fluorine giving it a partial negative charge.
Consequently, the bonding electrons are drawn away from the less electronegative carbon giving it a partial positive charge. The
the electron-rich fluorine is shown as red in the electrostatic potential map and while the electron-poor carbon is shown as blue.
The crossed arrow points in the direction of the electron-rich fluorine.

F𝛅− fluorine: EN = 4.0

𝛅+ carbon: EN = 2.5
H C H difference: 1.5
H

Electrostatic Potential Map and Dipole Moment of Fluoromethane

Chemists often use the term, inductive effect, to describe the shifting of electrons in a sigma by the electronegativity of atoms.
Relatively electronegative atoms, such as fluorine, tend to inductively draw electrons towards themselves and away from nearby
atoms. The inductive effect will be used to explain chemical reactivity in many situations in organic chemistry. An excellent
example of the inductive effect is seen when comparing the O-H bond polarities of water (H2O) and hypochlorous acid (ClOH).
Replacing the less electronegative hydrogen (EN = 2.1) in water with the more electronegative chlorine (EN = 3.0) in hypochlorous
acid creates a greater bond polarity. The chlorine draws electrons away giving the hydrogen a greater partial positive charge. This is
shown in the electrostatic potential map as an increase in the blue color around hydrogen.

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 O H O H
H Cl

water hypochlorous acid

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.
Many bonds between metals and non-metal atoms, are considered ionic, however some of these bonds cannot be simply identified
as one type of bond. Examples of this are the lithium - carbon bond in methyllithium which is usually considered as polar covalent
(somewhat between covalent and ionic) and the potassium - oxygen bond in potassium tert-butoxide which is considered more
ionic than covalent.

H CH3
H C Li H3C C O K

H CH3

methyllithium potassium tert-butoxide

Summary
Covalent bonds form when electrons are shared between atoms and are attracted by the nuclei of both atoms. In pure covalent
bonds, the electrons are shared equally. In polar covalent bonds, the electrons are shared unequally, as one atom exerts a stronger
force of attraction on the electrons than the other. The ability of an atom to attract a pair of electrons in a chemical bond is called its
electronegativity. The difference in electronegativity between two atoms determines how polar a bond will be. In a diatomic
molecule with two identical atoms, there is no difference in electronegativity, so the bond is nonpolar or pure covalent. When the
electronegativity difference is very large, as is the case between metals and nonmetals, the bonding is characterized as ionic.
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.

2. Which of the following elements is the more electronegative?

a) Br or C
b) C or H
c) Cl or I
d) C or Li
3. Which of the following molecules would you expect to have the more polarized O-H bond?

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4. Predict the direction of polarizing C-O bond in methanol by looking at its electrostatic potential map.

Solutions
1.

2.
a) Br
b) C
c) Cl
d) C
3.
The molecule on the right would have the more polorized O-H bond. The presence of the highly electronegative fluorines
would draw electrons away by the inductive effect.
4.

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)

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2.1: Polar Covalent Bonds - Electronegativity is shared under a CC BY-SA 4.0 license and was authored, remixed, and/or curated by Jim Clark,
Steven Farmer, Dietmar Kennepohl, Krista Cunningham, Tim Soderberg, Ed Vitz, & Ed Vitz.

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2.2: Polar Covalent Bonds - Dipole Moments
 Learning 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

In molecules containing more than one polar bond, the molecular dipole moment is just the vector combination of what can be regarded as individual
"bond 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. 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.

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.
The following is a simplified equation for a simple separated two-charge system that is present in diatomic molecules or when considering a bond
dipole within a molecule.

μdiatomic = Q × r (2.2.1)

This bond dipole, µ (Greek mu) is interpreted as the dipole from a charge separation over a distance r between the partial charges Q and Q (or the
+ −

more commonly used terms δ - δ ); the orientation of the dipole is along the axis of the bond. The units on dipole moments are typically debyes (D)
+ −

where one debye is equal to 3.336 x 1030 coulomb meters (C · m) in SI units. Consider a simple system of a single electron and proton separated by a
fix distance. The unit charge on an electron is 1.60 X 1019 C and the proton & electron are 100 pm apart (about the length of a typical covalent
bond), the dipole moment is calculated as:
μ = Qr

−19 −10
= (1.60 × 10 C )(1.00 × 10 m)

−29
= 1.60 × 10 C ⋅m (2.2.2)

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 1 D
−29
μ = (1.60 × 10 C ⋅ m) ( )
−30
3.336 × 10 C ⋅m

= 4.80 D (2.2.3)

4.80 D is a key reference value and represents a pure charge of +1 and -1 separated by 100 pm. However, if the charge separation were increased
then the dipole moment increases (linearly):
If the proton and electron were separated by 120 pm:
120
μ = (4.80 D) = 5.76 D (2.2.4)
100

If the proton and electron were separated by 150 pm:

150
μ = (4.80 D) = 7.20 D (2.2.5)
100

If the proton and electron were separated by 200 pm:

200
μ = (4.80 D) = 9.60 D (2.2.6)
100

 Example 2.2.1: Water

The water molecule in Figure 2.2.1 can be used to determine the direction and magnitude of the dipole moment. From the electronegativities of
oxygen and hydrogen, the difference is 1.2e for each of the hydrogen-oxygen bonds. Next, because the oxygen is the more electronegative atom,
it exerts a greater pull on the shared electrons; it also has two lone pairs of electrons. From this, it can be concluded that the dipole moment points
from between the two hydrogen atoms toward the oxygen atom. Using the equation above, the dipole moment is calculated to be 1.85 D by
multiplying the distance between the oxygen and hydrogen atoms by the charge difference between them and then finding the components of
each that point in the direction of the net dipole moment (the angle of the molecule is 104.5˚).
The bond moment of O-H bond =1.5 D, so the net dipole moment is
104.5˚
μ = 2(1.5) cos( ) = 1.84 D
2

Dipoles with Differing Atoms

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. The manner in which the individual bonds contribute to the dipole moment of the molecule is nicely
illustrated by the series of chloromethanes shown below. The electronegative chlorine draws electrons towards itself.

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

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, C H C l is a polar molecule (right panel in figure above). However, although a molecule
3

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. The hydrogen at the top of the molecule is less 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.

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 𝛅−
Cl
𝛅+ 𝛅𝛅+
Cl C Cl𝛅−
𝛅− +
𝛅+
Cl
𝛅−

𝛅+
H
𝛅−
𝛅+ 𝛅+
𝛅−
Cl C 𝛅+ Cl𝛅−
Cl
𝛅−

Figure 2.2.3 : Bond polarities for CCl4 (left) and CHCl3(right)

Electron densities in a molecule (and the dipole moments that unbalanced electron distributions can produce) are easily visualized with electrostatic
potential maps. In this example, C H C l , the blue area centered on carbon represents a electron-deficient positive area, of the molecule, the red area
3

centered on the chlorine, represents a electron-abundant negative area. This charge separation creates a net dipole moment of 1.87 D which points in
the direction of the chlorine. In, C C l the evenly spaced red areas represent that there is no separation of charge in the molecule. C C l has a net
4 4

dipole moment of zero which makes it a nonpolar molecule.

Cl Cl

H C H Cl C Cl
H Cl

chloromethane tetrachloromethane

(μ = 1.87 D) (μ = 0 D)

Figure 2.2.4 : Electrostatic potential maps and dipole moments for chloromethane and tetrachloromethane (carbon tetrachloride).
Molecules with asymmetrical charge distributions have 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.

Cl O Cl H F F
F F F
H Cl B C N C C F P S
H Cl Cl F F
Cl Cl H H H Cl Cl Cl F
H Cl F F

net dipole no net dipole net dipole net dipole no net dipole net dipole no net dipole no net dipole

HCl BCl3 CH2O NH3 CCl4 CHCl3 PF5 SF6

Figure 2.2.5 : Molecules with Polar Bonds. Individual bond dipole moments are indicated in black. Due to their different three-dimensional
structures, some molecules with polar bonds have a net dipole moment (HCl, CH2O, NH3, and CHCl3), indicated in red, whereas others do not
because the bond dipole moments cancel (BCl3, CCl4, PF5, and SF6).
Table 2.2.1: Dipole Moments of Some Compounds
Compound Dipole Moment (Debyes)

NaCl 9.0 (measured in the gas phase)

CH2O 2.33

CH3Cl 1.87

H2O 1.85

CH3OH 1.70

NH3 1.47

CH3NH2 1.31

CO2 0

CCl4 0

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 CH4 0

CH3CH3 0

The table above give the dipole moment of some common substances. Sodium chloride has the largest dipole listed (9.00 D) because it is an ionic
compounds. Even small organic compounds such as formaldehyde (CH2O, 2.33 D) and methanol (CH3OH, 1.70 D) have significant dipole moments.
Both of these molecules contain the strongly electronegative oxygen atom lone pair electrons which gives rise to considerable dipole moments.

H O
O
C
H H
H C H
H

methanol formaldehyde

(μ = 1.70 D) (μ = 2.33 D)

In contrast many organic molecule have a zero dipole moment despite the fact that they are made up of polar covalent bonds. In, structures with
highly symmetrical molecular geometries, the polar bonds and the lone pair electrons can can exactly cancel leaving no overall charge separation.
H
Cl H C H
O C O C
Cl C
Cl H
H
Cl H

carbon dioxide carbon tetrachloride ethane

(μ = 0 D) (μ = 0 D) (μ = 0 D)

 Exercise 2.2.1

Which of the molecules below have molecular dipole moments?

Answer
Only molecule (b) does not have a molecular dipole, due to its symmetry (bond dipoles are equal and in opposite directions). Add texts here.

 Exercise 2.2.2
Draw out the line structure of the molecule with a molecular formula of C2Cl4. Indicate all of the individual bond polarities and predict if the
molecule is polar or nonpolar.

Answer
Although the C–Cl bonds are rather polar, the individual bond dipoles cancel one another in this symmetrical structure, and
Cl2C=CCl2" id="MathJax-Element-47-Frame" role="presentation" style="position:relative;" tabindex="0">does not have a net dipole moment.

 Exercise 2.2.3

The following molecule has no net dipole moment, explain.

Answer
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.

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 Exercise 2.2.4

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

Answer
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.

 Exercise 2.2.1

Which molecule(s) has a net dipole moment?

a. H2S
b. NHF2
c. BF3

Answer
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:
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.

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.

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:

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Additional 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 C l
c. SO 2

d. [Math Processing Error]

e. [Math Processing Error]
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
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

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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.

2.2: Polar Covalent Bonds - Dipole Moments is shared under a CC BY-SA 4.0 license and was authored, remixed, and/or curated by Steven Farmer, Dietmar
Kennepohl, Krista Cunningham, Tim Soderberg, & Tim Soderberg.

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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.

Determining the Formal Charge on an Atom

A formal charge (F C ) 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:
1
F C = (# of valence electrons in free atom) − (# of lone-pair electrons) − (# of bonding electrons) (2.3.1)
2

To illustrate this method, let’s calculate the formal charge on the atoms in ammonia (NH ) whose Lewis structure is as follows:
3

H N H
H

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
1
F C (N ) = (5 valence electrons) − (2 lone pair electrons) − (6 bonding electrons)
2

=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
1
F C (H ) = (1 valence electrons) − (0 lone pair electrons) − (2 bonding electrons)
2

=0

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 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 NH molecule.
3

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 NH ion.

+
4

Given: chemical species

Asked for: formal charges
Strategy:
Identify the number of valence electrons in each atom in the NH ion. Use the Lewis electron structure of NH to identify the
+

4
+

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 NH ion is as follows:
+
4

H
H N H
H

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
1
F C (N ) = (5 valence electrons) − (0 lone pair electrons) − (8 bonding electrons)
2

= +1

Each hydrogen atom in has one bond and zero non-bonding electrons. The formal charge on each hydrogen atom is therefore
1
F C (H ) = (1 valence electrons) − (0 lone pair electrons) − (2 bonding electrons)
2

=0

The formal charges on the atoms in the NH ion are thus

+
4

0
H
0 1+ 0
H N H
H0

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 as the total charge of the ammonium polyatomic ion.

 Exercise 2.3.1

Write the formal charges on all atoms in BH .−

4

Answer

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 .

Determining the Charge of Atoms 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 (one of
the four nucleoside building blocks that make up DNA) using Equation 2.3.1. As you get more experience with organic structures,
you will be able to quickly look at this type of complicated structure and determine charges on each atom.
H H
H H C N
O C C H
H
C O N N
H C
C C
H H O
C C
H H
H O H

2'-deoxycytidine
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.
Organic chemistry only deals with a small part of the periodic table, so much so that it becomes convenient to be able to recognize
the bonding forms of these atoms. The figure below contains the most important bonding forms. These will be discussed in detail
below. An important idea to note is most atoms in a molecule are neutral. Pay close attention to the neutral forms of the elements
below because that is how they will appear most of the time.
Figure 2.3.1 : Structures of common organic atoms and ions.
Atom Positive Neutral Negative

C C
C C

N
N N N

O
O O O

Cl (halogens) Cl Cl Cl

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.
H OH H H
H C H H C H H H
H C C H H C C H
C C
H H H H H H

methane methanol ethane ethene ethyne

C or C or C

Carbon usually makes four bonds

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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 3
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 5 valence electrons and a formal charge of 1−.

C C C

carbon radical: 3 bonds & one unpaired

carbocation: 3 bonds & no lone pair carbanion: 3 bonds & one lone pair
electron

Two other possibilities are carbon 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 4 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. Though
carbenes are rare, you will encounter them in section 8.10 Addition of Carbenes to Alkenes.
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.
H

Neutral Hydrogen: one bond, no lone pair

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.

O O O O O

neutral oxygen: 2 bonds & 2 lone pairs negative oxygen: 1 bond & 3 lone pairs positive oxygen: 3 bonds & one lone pair

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+.
Oxygen can also exist as a radical, such as where an oxygen atom has one bond, two lone pairs, 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 most oxygen containing molecules you will encounter in organic chemistry.

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

N N N N N N
N

neutral nitrogen: 3 bonds & 1 lone pair positive nitrogen: 4 bonds negative nitrogen: 2 bonds & 2 lone pairs

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.

Phosphorus and Sulfur

Two third row elements are commonly found in biological organic molecules: phosphorus and sulfur. 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 (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.
O
O P O
O

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+.

F Cl Br I

Common Neutral Bonding Patterns for Halogens

Br

Common Positive Bonding Pattern for Halogens

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.

 Exercise 2.3.2

Please identify an atom with a non-neutral charge in the following atom:

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 Answer

Drawing the Lewis Structure of Ionic Molecular Compounds

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. By changing the number of valence electrons the bonding characteristic of oxygen are now
changed. Now the oxygen has three non-bonding lone pairs, and can only form one bond to a hydrogen.

H O H O H O or H O

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 to give oxygen five valence electrons. The oxygen has one non-bonding lone pair
and three unpaired electrons which can be used to form bonds to three hydrogen atoms.
H H H
H
H O H H O H H O H or H O H

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:
O C O

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:
O C O or O C O

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:
O C O or O C O
0 0 0 1− 0 1+

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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
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: Thiocyanate Ion

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:
S C N S C N S C N

(a) (b) (c)

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 2.3.2: Fulminate Ion

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 the most stable.

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Exercises
1. Draw the Lewis structure of each of these molecules: CH , NH , CH , NH , BF . In each case, use the method of
+

3
−
2
−

3
+
4
−
4

calculating formal charge described to satisfy yourself that the structures you have drawn do in fact carry the charges shown.
Answer
1.

Questions
Q2.3.1
Give the formal charges for all non-hydrogen atoms in the following molecules: BH , H −

4 2
O , CH
3
O
−

Solutions

S2.3.1
BH4− (B = −1)
H2O (O = 0)
CH3O− (C = 0, O = −1)

2.3: Formal Charges is shared under a CC BY-SA 4.0 license and was authored, remixed, and/or curated by Steven Farmer, Dietmar Kennepohl,
Layne Morsch, Krista Cunningham, Tim Soderberg, William Reusch, & William Reusch.

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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

Resonance 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 contributors or canonical forms). Resonance contributors involve the
‘imaginary movement’ of pi-bonded electrons or of lone-pair electrons that are adjacent to pi bonds. Note, sigma bonds cannot be
broken during resonance – if you show a sigma bond forming or breaking, you are showing a chemical reaction taking place.
Likewise, the positions of atoms in the molecule cannot change between resonance contributors.
When looking at the structure of the molecule, formate, we see that there are two equivalent structures possible. Which one is
correct? There are two simple answers to this question: 'both' and 'neither one'. Both ways of drawing the molecule are equally
acceptable approximations of the bonding picture for the molecule, but neither one, by itself, is an accurate picture of the
delocalized pi bonds. The two alternative drawings, however, when considered together, give a much more accurate picture than
either one on its own. This is because they imply, together, that the carbon-carbon bonds are not double bonds, not single bonds,
but about halfway in between.
O O

H O H O

Formate Ion Structures are Equivalent in Energy

When it is possible to draw more than one valid structure for a compound or ion, we have identified resonance contributors: two
or more different Lewis structures depicting the same molecule or ion that, when considered together, do a better job of
approximating delocalized pi-bonding than any single structure. By convention, resonance contributors are linked by a double-
headed arrow, and are sometimes enclosed by brackets:
double-headed
‘resonance arrow’

O O

H O H O

resonance resonance
contributor A contributor B

The depiction of formate using the two resonance contributors A and B in the figure above does not imply that the molecule at one
moment looks like structure A, then at the next moment shifts to look like structure B. Rather, at all moments, the molecule is a
combination, or resonance hybrid of both A and B. Each individual resonance contributor of the formate ion is drawn with one
carbon-oxygen double bond (120 pm) and one carbon-oxygen single bond (135 pm), with a negative formal charge located on the
single-bonded oxygen. However, the two carbon-oxygen bonds in formate are actually the same length (127 pm) which implies that
neither resonance contributor is correct. Although there is an overall negative formal charge on the formate ion, it is shared equally

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between the two oxygens. Therefore, the formate ion can be more accurately depicted by a pair of resonance contributors.
Alternatively, a single structure can be used, with a dashed line depicting the resonance-delocalized pi bond and the negative charge
located in between the two oxygens.
−½
O O
−½
H O H O

The electrostatic potential map of formate shows that there is an equal amount of electron density (shown in red) around each
oxygen.

Valence bond theory can be used to develop a picture of the bonding in a carboxylate group. We know that the carbon must be sp2-
hybridized, (the bond angles are close to 120˚, and the molecule is planar), and we will treat both oxygens as being sp2-hybridized
as well. Both carbon-oxygen sigma bonds, then, are formed from the overlap of carbon sp2 orbitals and oxygen sp2 orbitals.

In addition, the carbon and both oxygens each have an un-hybridized 2pz orbital situated perpendicular to the plane of the sigma
bonds. These three 2pz orbitals are parallel to each other, and can overlap in a side-by-side fashion to form a delocalized pi bond.

O O

H O H O

resonance resonance
contributor A contributor B

Overall, the situation is one of three parallel, overlapping 2pz orbitals sharing four delocalized pi electrons. Because there is one
more electron than there are 2pz orbitals, the system has an overall charge of 1–. Resonance contributors are used to approximate
overlapping 2pz orbitals and delocalized pi electrons. Molecules with resonance are usually drawn showing only one resonance
contributor for the sake of simplicity. However, identifying molecules with resonance is an important skill in organic chemistry.

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This example shows an important exception to the general rules for determining the hybridization of an atom. The oxygen with the
negative charge appears to be sp3 hybridized because it is surrounded by four electron groups. However, this representation of the
oxygen atom is not correct because it is actually part of a resonance hybrid. A pair of lone pair of electrons on the negatively
charged oxygen are not localized in an sp3 orbital, rather, they are delocalized as part of a conjugated pi system. The stability
gained though resonance is enough to cause the expected sp3 to become sp2. The sp2 hybridization gives the oxygen a p orbital
allowing it to participate in conjugation. As a general rule sp3 hybridized atoms with lone pair electrons tend to become sp2
hybridized when adjacent to a conjugated system.
lone pair is in lone pair is in
a p orbital an sp 3 orbital

H O H 3C O

O is sp 2 O is sp 3

oxygen is conjugated oxygen is not conjugated

Example: Carbonate (CO32−)

Like formate, 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:
O
C
O O

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:

O
C
O O

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−
O
C
O O

5. There are no electrons 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:
2− 2− 2−
O O O
C C C
O O O O O O

As with formate, 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:
2− 2− 2−
O O O
C C C
O O O O O O

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As the case for formate, 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:
H
H C H
C C
C C
H C H
H

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:
H
H C H
C C
C C
H C H
H

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:
H H
H C H H C H
C C C C
and
C C C C
H C H H C H
H H

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:

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 H H
H C H H C H
C C C C
C C C C
H C H H C H
H H

benzene

This combination of p orbitals for benzene can be visualized as a ring with a node in the plane of the carbon atoms. As can be
seen in an electrostatic potential map of benzene, the electrons are distributed symmetrically around the ring.

 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

Exercises
Questions
Q2.4.1
Draw the resonance structures for the following molecule:

Solutions
S2.4.1

Extra example - O3
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°.

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

O
O O

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

O
O O

with 14 electrons left over.

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

O
O O

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:

O
O O

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

O or O
O O O O

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:

O O
O O O O

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.

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2.4: Resonance is shared under a CC BY-SA 4.0 license and was authored, remixed, and/or curated by Steven Farmer, Dietmar Kennepohl, Layne
Morsch, Krista Cunningham, Tim Soderberg, & Tim Soderberg.

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2.5: Rules for Resonance Forms
 Objectives

After completing this section, you should be able to

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 Drawing and Working with Resonance Contributors

Recognizing, drawing, and evaluating the relative stability of resonance contributors is essential to understanding organic reaction
mechanisms. When learning to draw and interpret resonance structures, there are a few basic guidelines to help. .
1) There is ONLY ONE REAL STRUCTURE for each molecule or ion. This real structure (the resonance hybrid) takes its
character from the average of all the individual resonance contributors. When looking at a resonance contributors, we are
seeing the exact same molecule or ion depicted in different ways. Resonance hybrids are really a single, unchanging
structure.
O O

H O H O

Major resonance contributors of the formate ion

−½
O O
−½
H O H O

Representations of the formate resonance hybrid

2) The resonance hybrid is more stable than any individual resonance structures. Often, resonance structures represent the
movement of a charge between two or more atoms. The charge is spread out amongst these atoms and therefore more
stabilized. When looking at the picture above the resonance contributors represent the negative charge as being on one
oxygen or the other. The resonance hybrid shows the negative charge being shared equally between two oxygens. In the
resonance hybrid, the negative charge is spread out over a larger part of the molecule and is therefore more stable.
3) Resonance contributors do not have to be equivalent. Because of this, resonance structures do necessarily contribute
equally to the resonance hybrid. The two resonance structures shown below are not equivalent because one show the
negative charge on an oxygen while the other shows it on a carbon. Later, we will show that the contributor with the negative
charge on the oxygen is the more stable of the two. Also, this means that the resonance hybrid will not be an exact mixture of
the two structures.
O O
C C
H3C CH2 H3C CH2

4) All resonance contributors must be correct Lewis structures. Each atom should have a complete valence shell and be
shown with correct formal charges. A carbocation (carbon with only 6 valence electrons) is the only allowed exception to the
valence shell rules. The structure below is an invalid resonance structure even though it only shows the movement of a pi
bond. The resulting structure contains a carbon with ten electrons, which violates the octet rule, making it invalid.
10 electrons on carbon!
???
H2C CH3 H2C CH3
C C
H incorrect! H

5) All resonance contributors must have the same molecular formula, the same number of electrons, and same net charge.
The molecules in the figure below are not resonance structures of the same molecule because then have different molecular
formulas (C2H5NO Vs. C2H6NO). Also, the two structures have different net charges (neutral Vs. positive).

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 O OH
C H C H
H3 C N incorrect! H3C N
H H

6) Resonance contributors only differ by the positions of pi bond and lone pair electrons. Sigma bonds are never broken or
made, because of this atoms must maintain their same position. The molecules in the figure below are not resonance
structures of the same molecule even though they have the same molecular formula (C3H6O). These molecules are
considered structural isomers because their difference involves the breaking of a sigma bond and moving a hydrogen atom.
H
O O
C H C H
H 3C C incorrect! H 3C C
H
H H

Major and Minor Resonance Contributors

As previously state the true structure of a resonance hybrid is the combination of all the possible resonance structures. If the
resonance structures are equal in stability they the contribute equally to the structure of the hybrid. However, if the resonance
structures have different stabilities they contribute to the hybrid's structure in proportions related to their relative stabilities. It can
be said the the resonance hybrid's structure resembles the most stable resonance structure. Because of this it is important to be able
to compare the stabilities of resonance structures. In the example below, structure B is much less important in terms of its
contribution to the hybrid because it contains the violated octet of a carbocation. The relative stabilities of the two structures are so
vastly different that molecules which contain a C=O bond are almost exclusively written in a form like structure A. However, as
will learn in chapter 19, the positively charged carbon created by structure B will explain how the C=O bond will react with
electron rich species.

O O O 𝛅−
C C C
H H H H H 𝛅+ H
A B
major minor hybrid representation
contributor contributor as a polar structure

Rules for Estimating Stability of Resonance Structures

1. The resonance structures in which all atoms have complete valence shells is more stable. This means most atoms have a full
octet. In the example below structure A has a carbon atom with a positive charge and therefore an incomplete octet. Based on this
criterion, structure A is less stable and is a more minor contributor to the resonance hybrid than structure B.
H3 C H H3 C H
C O C O
H3 C H3 C

A B

2. The structures with the least number of formal charges is more stable. Based on this, structure B is less stable because is has
two atoms with formal charges while structure A has none. Structure A would be the major resonance contributor.

O O
H 2C C H2C C
C H C H
H H

A B

3. The structures with a negative charge on the more electronegative atom will be more stable. The difference between the two
resonance structures is the placement of a negative charge. Structure B is the more stable and the major resonance contributor,
because it places the negative charge on the more electronegative oxygen.

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 O O
C H C H
H 3C C H 3C C
H H

A B

4. The structures with a positive charges on the least electronegative atom (most electropositive) is more stable.
5. The structures with the least separation of formal charges is more stable. The only difference between the two structures below
are the relative positions of the positive and negative charges. In structure A the charges are closer together making it more stable.
H H H H
C H C H
C C C C
H C H H C H
H H
A B

6. Resonance forms that are equivalent have no difference in stability. When looking at the two structures below no difference
can be made using the rules listed above. This means the two structures are equivalent in stability and would make equal structural
contributions to the resonance hybrid.
O O
C C
H O H O

A B

Examples of major and minor contributors

Example 1:

O O
H C H C
N CH3 N CH3
H H
major contributor minor contributor
(neutral structure) (charge separation)

Example 2:

CH3 CH3
H C H C
N CH3 N CH3
H H

major contributor
minor contributor (All atoms have octets, even though
(Incomplete octet on there is a positive charge on nitrogen.)
carbon.)

Example 3:

H 3C C O H 3C C O

minor contributor major contributor

(Incomplete octet on carbon, but (All atoms have octets, even though there is a
more important in terms of reactivity.) positive charge on oxygen.)

Carboxylate example
In the case of carboxylates, contributors A and B below are equivalent in terms of their relative contribution to the hybrid structure.
However, there is also a third resonance contributor C, in which the carbon bears a positive formal charge (a carbocation) and both

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oxygens are single-bonded and bear negative charges.

O O O
C C C
H O H O H O

A B C
minor contributor
(separation of charge)

Structure C makes a less important contribution to the overall bonding picture of the group relative to A and B. How do we know
that structure C is the ‘minor’ contributor? Apply the rules below

The carbon in contributor C does not have an octet. In general, resonance contributors in which a carbon does not fulfill the
octet rule are relatively less important. (rule #1)
In structure C, there are only three bonds, compared to four in A and B. In general, a resonance structure with a lower
number of total bonds is relatively less important. (rule #2)
Structure C also has more formal charges than are present in A or B. In general, resonance contributors in which there is
more/greater separation of charge are relatively less important. (rule #3)
Structures A and B are equivalent and will be equal contributors to the resonance hybrid. (rule #5).
The resonance contributor in which a negative formal charge is located on a more electronegative atom, usually oxygen or
nitrogen, is more stable than one in which the negative charge is located on a less electronegative atom such as carbon. An
example is in the upper left expression in the next figure. (rule #4)

Example with 3 resonance structures

Molecules with more than 2 resonance structures can also be considered using the rules listed above. Of the resonance structures
listed below, structure A would be the most stable because all the non-hydrogen atoms have a full octet and the negative charge is
on the more electronegative atom (oxygen). Structure C would be next in stability because all of the non-hydrogen atoms have full
octets, though now the negative charge is on carbon rather than oxygen. Structure B would be the least stable of the three because it
has the carbocation does not have an octet. Of the three, structure A would be the major resonance structure and would most
resemble the structure of the true resonance hybrid. Structure B is considered a minor resonance contributor and would have very
little effect on the structure of the resonance hybrid.

H3 C C N O H3C C N O H3C C N O

A B C

 Example 2.5.1

Draw the major resonance contributor of the structure below. Include in your figure the appropriate curved arrows showing
how you got from the given structure to your structure. Explain why your contributor is the major one. In what kind of orbitals
are the two lone pairs on the oxygen?

2 4 5
1 3 O

Solution
In the structure above, the carbon with the positive formal charge does not have a complete octet of valence electrons. Using
the curved arrow convention, a lone pair on the oxygen can be moved to the adjacent bond to the left, and the electrons in the
double bond shifted over to the left (see the rules for drawing resonance contributors to convince yourself that these are 'legal'
moves).

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 O O

minor major
(Carbon does not have (All atoms have a
a complete octet.) complete octet.)

The resulting resonance contributor, in which the oxygen bears the formal charge, is the major one because all atoms have a
complete octet, and there is one additional bond drawn (resonance rules #1 and #2 both apply). This system can be thought of
as four parallel 2p orbitals (one each on C2, C3, and C4, plus one on oxygen) sharing four pi electrons. One lone pair on the
oxygen is in an unhybridized 2p orbital and is part of the conjugated pi system, and the other is located in an sp2 orbital.
Also note that one additional contributor can be drawn, but it is also minor because it has a carbon with an incomplete octet:

minor

Exercises
1) For the following resonance structures please rank them in order of stability. Indicate which would be the major contributor to
the resonance hybrid.

2) Draw four additional resonance contributors for the molecule below. Label each one as major or minor (the structure below is of
a major contributor).

3) Draw three resonance contributors of methyl acetate (an ester with the structure CH3COOCH3), and order them according to
their relative importance to the bonding picture of the molecule. Explain your reasoning.
4) Below is a minor resonance contributor of a species known as an ‘enamine’, which we will study more in Section 19.8
(formation of enamines) Section 23.12 (reactions of enamines). Draw the major resonance contributor for the enamine, and explain
why your contributor is the major one.

5) Draw the major resonance contributor for each of the anions below:

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Solutions
1) Structure I would be the most stable because all the non-hydrogen atoms have a full octet and the negative charge is on the more
electronegative nitrogen. Structure III would be the next in stability because all of the non-hydrogen atoms have full octets.
Structrure II would be the least stable because it has the violated octet of a carbocation.
2)

3)

The contributor on the left is the most stable: there are no formal charges.
The contributor on the right is least stable: there are formal charges, and a carbon has an incomplete octet.
The contributor in the middle is intermediate stability: there are formal charges, but all atoms have a complete octet.
4) This contributor is major because there are no formal charges.

5)

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Exercises
Questions
Q2.5.1
Are all the bond lengths the same in the carbonate ion, CO32-?

Solutions
S2.5.1 Yes, the bond lengths in carbonate ion are all the same. Carbonate ion exists as the resonance hybrid of the three resonance
forms below.

Additional resonance topics

Recognizing Resonance
Resonance contributors involve the ‘imaginary movement’ of pi-bonded electrons or of lone-pair electrons that are adjacent to (i.e.
conjugated to) pi bonds. You can never shift the location of electrons in sigma bonds – if you show a sigma bond forming or
breaking, you are showing a chemical reaction taking place. Likewise, the positions of atoms in the molecule cannot change
between two resonance contributors.
Because benzene will appear throughout this course, it is important to recognize the stability gained through the resonance
delocalization of the six pi electrons throughout the six carbon atoms. Benzene also illustrates one way to recognize resonance -
when it is possible to draw two or more equivalent Lewis structures. If we were to draw the structure of an aromatic molecule such
as 1,2-dimethylbenzene, there are two ways that we could draw the double bonds:
CH3 CH3
CH3 CH3

Is this correct… …or is this?

Which way is correct? There are two simple answers to this question: 'both' and 'neither one'. Both ways of drawing the molecule
are equally acceptable approximations of the bonding picture for the molecule, but neither one, by itself, is an accurate picture of
the delocalized pi bonds. The two alternative drawings, however, when considered together, give a much more accurate picture

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than either one on its own. This is because they imply, together, that the carbon-carbon bonds are not double bonds, not single
bonds, but about halfway in between.
When it is possible to draw more than one valid structure for a compound or ion, we have identified resonance contributors: two
or more different Lewis structures depicting the same molecule or ion that, when considered together, do a better job of
approximating delocalized pi-bonding than any single structure. By convention, resonance contributors are linked by a double-
headed arrow, and are sometimes enclosed by brackets:
double-headed
“resonance arrow”
CH3 CH3
CH3 CH3

resonance resonance
contributor A contributor B

In order to make it easier to visualize the difference between two resonance contributors, small, curved arrows are often used. Each
of these arrows depicts the ‘movement’ of two pi electrons. In the drawing of resonance contributors, however, this electron
‘movement’ occurs only in our minds, as we try to visualize delocalized pi bonds. Nevertheless, use of the curved arrow notation is
an essential skill that you will need to develop in drawing resonance contributors.
The depiction of benzene using the two resonance contributors A and B in the figure above does not imply that the molecule at one
moment looks like structure A, then at the next moment shifts to look like structure B. Rather, at all moments, the molecule is a
combination, or resonance hybrid of both A and B.
Caution! It is very important to be clear that in drawing two (or more) resonance contributors, we are not drawing two different
molecules: they are simply different depictions of the exact same molecule. Furthermore, the double-headed resonance arrow
does NOT mean that a chemical reaction has taken place.
Benzene is often drawn as only one of the two possible resonance contributors (it is assumed that the reader understands that
resonance hybridization is implied). However, sometimes benzene will be drawn with a circle inside the hexagon, either solid or
dashed, as a way of drawing a resonance hybrid.

resonance contributor drawings resonance hybrid drawings

Examples of Resonance
Molecules with a Single Resonance Configuration
Example 1:

O O
O O O O

Example 2:

Example 3:

O O

H3C N H3C N

Example 4:

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 H H
O O

N N
O O O O

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:

O O O O O O
N N N
O O O

O O O O O O
C C C
O O O

H N H N H N
C N C N C N
H H H

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.
Hybrid Resonance

Cl Cl Cl Cl Cl

The different resonance forms of the molecule help predict the reactivity of the molecule at specific sites.
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.

2.5: Rules for Resonance Forms is shared under a CC BY-SA 4.0 license and was authored, remixed, and/or curated by Steven Farmer, Dietmar
Kennepohl, Krista Cunningham, Tim Soderberg, William Reusch, & William Reusch.

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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

Curved Arrows Communicate Electron Flow (movement)

Organic chemistry has developed a system to show how electrons move between resonance structures. This system will also be
used to help describe how electrons from in reactions. Curved double barbed arrows indicates the flow of two electrons. The base
of the curved arrow is placed at the source of the electrons that are moving. The head of the arrow is placed at the destination of the
electrons.

electron electron
source destination

double barb for 2e⊝

It is also important to consciously use the correct type of arrow. There are four primary types of arrows used by chemists to
communicate one of the following: completion reaction, equilibrium reaction, electron movement, and resonance forms. The three
other types of arrows are shown below to build discernment between them. Note, the electron movement arrows are the only ones
that are curved.
Reaction Arrows
reactants products reactants products
completion equilibrium

Resonance Arrows

O O

O resonance O

Using Curved Arrows to Show Electron Movement

Because the double barbed arrow represents the movement of two electrons, they usually involve lone pair electrons or pi bonds.
There are only three types of electron "motion" in resonance. They are:

1. A lone pair forms a pi bond to an adjacent atom

2. A pi bond forms a new pi bond to an adjacent atom
3. A pi bond forms a lone pair on adjacent atom

Let's look at the resonance within acrylic acid to demonstrate these three types of resonance.

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 acrylic acid

H O H O H O H O
C C H C C H C C H C C H
H C O H C O H C O H C O
H H H H

A B C D

The curved arrow in structure A represents the type 3 resonance "motion" - the pi bond between the carbon and oxygen breaks to
form another lone pair on the oxygen. The curved arrow in structure B represents type 2 resonance "motion" - the pi bond breaks to
form a new pi bond to the carbocation carbon. In structure C, there are two curved arrows. The curved arrow from the oxygen lone
pair is type 1 resonance motion - the lone pairs forms a new pi bond between the oxygen and carbon. The other arrow in structure C
moves the pi bond to the end of the chain and represents resonance type 2. By combining these three basic types of electron
movement we can describe virtually any type of resonance.

Example:
Below are a few more examples of ‘legal’ resonance expressions. Confirm for yourself that the octet rule is not exceeded for any
atoms, that formal charges are correct, and identify which type of electron movement is being represented by each arrow.

O O
O CH3 O CH3
C H C H H 3C C H 3C C
H 3C C H 3C C
H H
H H

H O H O
C C C C
H C H H C H
H H

 Exercise 2.6.1

Draw the resonance contributors that correspond to the curved, two-electron movement arrows in the resonance expressions
below. Then identify the type of resonance motion in each structure below.

Answer

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  Exercise 2.6.2

In each resonance expression, identify the type of resonance motion. Then draw curved arrows on the left-side contributor that
shows how we get to the right-side contributor.

Answer

Recognizing Common Patterns of Resonance

If you examine a large number of resonance examples, you will begin to notice that they nearly always match common patterns, of
which there are only three. It is important to be able to identify atoms that participate in resonance. In complex resonance cases,
multiple types of resonance may occur simultaneously.
Type I - Neutral Species
The electrons of a pi bond move to become a set of lone pair electrons on a electronegative atom. The resonance structure made has
a carbon with a violated octet which make it a minor contributor. This type of resonance is commonly used to the polarity in certain
double bonds.
Neutral Species
Y Type 1 Y
C C

major minor
(no octet on C)

Note: Y is an electronegative atom, usually N, O, or S.

 Type I Example

O O
C C
H H H H
major minor

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Type II - Charged Species
Type II resonance is only seen with a + charge, and usually involves a positive charge on oxygen or nitrogen being shared onto a
carbon; the carbocation form has only six valence electrons on the carbon, so it is a less stable form than the major form (which has
complete octets).
Charged Species
Y Type 2 Y
C C

major minor
(no octet on C)

Note: Y is an electronegative atom, usually N, O, S, sometimes halogen

 Type II Example
H H
N H N H
H O H O
C H C H
H H

major major

Type III - Allylic Resonance

Type III resonance is very common and important because is serves to stabilize positive charges, negative charges, or lone pairs. It
is sometimes referred to as “allylic” resonance, especially in cases with all carbon. This type of resonance can be identified by a
three-atom group of atoms each with sp2 hybridization and a p orbital.
Type 3
Y Y
X Z* *X Z
* represents a charge or an unpaired electron

 Type III Example

Atoms with lone pair electrons next to a pi bond can be sp2 hybridized and have the lone pair of electrons in a p orbital despite
the fact that they are surrounded by four electron groups. The lone pair electrons contained in the p orbital cause the ion to be
stabilized due to resonance.

O O
C H C H
H C H 3C C
H H

O O
C C
H O H3 C O

O O
C CH3 C CH3
H 3C N H 3C N
H H

Similarly, carbocations are sp2-hybridized, with an empty 2p orbital oriented perpendicular to the plane formed by three sigma
bonds. If a carbocation is adjacent to a double bond, then three 2p orbitals can overlap and share the two pi electrons - another kind

2.6.4 https://chem.libretexts.org/@go/page/31388
of conjugated pi system in which the positive charge is shared over two carbons.
charge is delocalized over two carbons
H H H H
C C C C
H C H H C H
H H

empty p orbital empty p orbital

H H H H
H H H H
H H

three p orbitals sharing two pi electrons

 Exercise 2.6.3
Each of the 'illegal' resonance expressions below contains one or more mistakes. Explain what is incorrect in each.

Answer
The first pair are not resonance structures since there is an additional hydrogen on the second structure oxygen. The second
pair pushed electrons toward nitrogen which already has a lone pair and would exceed its octet. The third pair includes a
structure with 5 bonds to carbon. The fourth pair requires moving carbon-hydrogen bonds, therefore is not resonance. The
fifth pair show electrons moving toward the negatively charged oxygen which would exceed an octet. The fifth pair shows
a sigma bond breaking on the ring, rather than pi bond.

 Exercise 2.6.4

a) Draw three additional resonance contributors for the carbocation below. Include in your figure the appropriate curved arrows
showing how one contributor is converted to the next.

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b) Fill in the blanks: the conjugated pi system in this carbocation is composed of ______ 2p orbitals sharing ________
delocalized pi electrons.

Answer
a)

b) The conjugated pi system in this carbocation is composed of seven p orbitals containing six delocalized pi electrons.

 Example 2.6.1

Draw the major resonance contributor of the structure below. Include in your figure the appropriate curved arrows showing
how you got from the given structure to your structure. Explain why your contributor is the major one. In what kind of orbitals
are the two lone pairs on the oxygen?

4 5
2
1 3
O

Solution
In the structure above, the carbon with the positive formal charge does not have a complete octet of valence electrons. Using
the curved arrow convention, a lone pair on the oxygen can be moved to the adjacent bond to the left, and the electrons in the
double bond shifted over to the left (see the rules for drawing resonance contributors to convince yourself that these are 'legal'
moves).

O O

minor major

The resulting resonance contributor, in which the oxygen bears the formal charge, is the major one because all atoms have a
complete octet, and there is one additional bond drawn (resonance rules #1 and #2 both apply). This system can be thought of
as four parallel 2p orbitals (one each on C2, C3, and C4, plus one on oxygen) sharing four pi electrons. One lone pair on the
oxygen is in an unhybridized 2p orbital and is part of the conjugated pi system, and the other is located in an sp2 orbital.
Also note that one additional contributor can be drawn, but it is also minor because it has a carbon with an incomplete octet:

minor

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 Exercise 2.6.5
The figure below shows how the negative formal charge on an oxygen (of an enol) can be delocalized to the carbon indicated
by an arrow. More resonance contributors can be drawn in which negative charge is delocalized to three other atoms on the
molecule.
a) Circle these atoms that can also have a resonance structure with a negative charge.
b) Draw the two most important resonance contributors for the enolate ion.

Answer
The two major contributors are those in which the negative formal charge is located on an oxygen rather than on a carbon.

Exercise 2.6.5:
a) Draw three additional resonance contributors for the carbocation below. Include in your figure the appropriate curved arrows
showing how one contributor is converted to the next.

b) Fill in the blanks: the conjugated pi system in this carbocation is composed of ______ 2p orbitals sharing ________
delocalized pi electrons.
Exercise 2.6.6: Draw the major resonance contributor for each of the anions below.

c) Fill in the blanks: the conjugated pi system in part (a) is composed of ______ 2p orbitals containing ________ delocalized pi
electrons.
Exercise 2.6.7: The figure below shows how the negative formal charge on the oxygen can be delocalized to the carbon
indicated by an arrow. More resonance contributors can be drawn in which negative charge is delocalized to three other atoms
on the molecule.
a) Circle these atoms.
b) Draw the two most important resonance contributors for the molecule.

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 A word of advice
Becoming adept at drawing resonance contributors, using the curved arrow notation to show how one contributor can be
converted to another, and understanding the concepts of conjugation and resonance delocalization are some of the most
challenging but also most important jobs that you will have as a beginning student of organic chemistry. If you work hard now
to gain a firm grasp of these ideas, you will have come a long way toward understanding much of what follows in your organic
chemistry course. Conversely, if you fail to come to grips with these concepts now, a lot of what you see later in the course
will seem like a bunch of mysterious and incomprehensible lines, dots, and arrows, and it will be difficult to be successful in
organic chemistry.

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:
pkukmweb.ukm.my/~mbz/c_penerb...83%29/p329.pdf

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

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.

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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).

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

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

2.6.9 https://chem.libretexts.org/@go/page/31388
7. The resonance hybrid for NO3-, hybrid bonds are in red.

2.6: Drawing Resonance Forms is shared under a CC BY-SA 4.0 license and was authored, remixed, and/or curated by Steven Farmer, Dietmar
Kennepohl, Layne Morsch, Krista Cunningham, Kelly Matthews, Sharon Wei, Liza Chu, & Liza Chu.

2.6.10 https://chem.libretexts.org/@go/page/31388
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-Lowry 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 C l + 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.
Bronsted-Lowry Acids and Bases

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 HCO3 + HOH H2CO3 + OH

base acid

HCO3 + HOH H2CO3 + OH

conjugate conjugate
acid base

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.

proton gained proton lost

H
H Cl + O H O H + Cl
H H

HCl(aq) H2O(l) H3O (aq) Cl (aq)

parent acid parent base conjugate acid conjugate base

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).

proton gained proton lost

O H O
C H+ O H O H + C
H3C O H H H3C O

CH3CO2H(aq) H2O(l) H3O (aq) CH3CO2 (aq)

parent acid parent base conjugate acid conjugate base

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-.

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 proton gained proton lost

H
+ O H N H + O
N H
H H H H H
H
NH3(aq) H2O(l) NH4 (aq) OH(aq)
parent base parent acid conjugate acid conjugate base

 Example 2.7.1

Aniline (C6H5NH2) is slightly soluble in water. It has a nitrogen atom that can accept a hydrogen ion from a water molecule
just like the nitrogen atom in ammonia does. Write the chemical equation for this reaction and identify the Brønsted-Lowry
acid and base.

Solution
C6H5NH2 and H2O are the reactants. When C6H5NH2 accepts a proton from H2O, it gains an extra H and a positive charge and
leaves an OH− ion behind. The reaction is as follows:
+ −
C H NH (aq) + H O(ℓ) −
↽⇀
− C H NH (aq) + OH (aq)
6 5 2 2 6 5 3

Because C6H5NH2 accepts a proton, it is the Brønsted-Lowry base. The H2O molecule, because it donates a proton, is the
Brønsted-Lowry acid.

 Example 2.7.1

Identify the conjugate acid-base pairs in this equilibrium.

+ −
(C H3 )3 N + H2 O ⇌ (C H3 )3 N H + OH

Solution
One pair is H2O and OH−, where H2O has one more H+ and is the conjugate acid, while OH− has one less H+ and is the
conjugate base.
The other pair consists of (CH3)3N and (CH3)3NH+, where (CH3)3NH+ is the conjugate acid (it has an additional proton) and
(CH3)3N is the conjugate base.

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

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Exercises
1. Identify the Brønsted-Lowry acids and bases in the reactions given below.
a. C H 3C H 2 O
−
+ H 2O <=> C H 3C H 2OH + OH
−

b. C H 3C H 2OH + H 2SO4 <=> C H 3C H 2OH 2 + +H SO4−

2. Show the structures of species X and Y in the following acid-base reactions:

Answer:
1. a.

b.

2. a)

b)

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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:

2.7: Acids and Bases - The Brønsted-Lowry Definition is shared under a CC BY-SA 4.0 license and was authored, remixed, and/or curated by
Steven Farmer, Dietmar Kennepohl, Krista Cunningham, Tim Soderberg, & Tim Soderberg.

2.7.5 https://chem.libretexts.org/@go/page/31389
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.
O
HO S OH
O

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.

O O H
+ O +
C H H H C O
H 3C O H3C O H H

H A B A H B
acetic acid water acetate ion hydronium ion

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.

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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:
− +
a − ⋅a +
[C H3 C OO ][ H3 O ]
C H3 C OO H3 O
Keq = ≈ (2.8.1)
aC H3 C OOH ⋅ aH2 O [C H3 C OOH ][1]

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

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
O H H H
O
HO S O H Cl H O R O
O H H R R H
hydrochloric acid hydronium protonated alcohol
sulfuric acid protonated ketone
pKa −7 pKa 0.00 pKa ~ −3
pKa −10 pKa ~ −7
H
O O O H O
N
RO P O RO P O HO P O H H
OH H OR H OH H R O

phosphate monoester phosphate diester phosphoric acid protonated aniline carboxylic acid
pKa ~ 1 pKa ~ 1.5 pKa 2.2 pKa ~ 4.6 pKa ~ 4-5

H O H O
N H
H H N C H H N H
O O H
hydrogen cyanide
pyridinium carbonic acid ammonium phenol
pKa ~ 9.2
pKa 5.3 pKa 6.4 pKa 9.2 pKa 9.9

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 O O
R S H O H R O R
H H R N H R
H H R
thiol water alcohol
amide alpha-proton
pKa ~ 10-11 pKa 14.00 pKa ~ 16-18
pKa ~ 17 pKa ~ 18-20
R R H
R C C H C C H N
R H H
terminal alkyne
terminal alkene ammonia
pKa ~ 25
pKa ~ 35 pKa ~ 35

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 pKa values 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 = 14.00).

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 pKa of 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.
HO
O

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

Hd
Hc Hc

pKa Ha ~ 10
pKa Hb = not on table (not acidic)
pKa Hc ~ 19
d
pKa H = not on table (not acidic)
Aldehyde and aromatic protons are not at all acidic (pKa values 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.

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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.
a) H c)
O OH
O e)
O OH
NH3 SH

N
CH3
H
O
b) O d)

NH2 NH2 N
OH H
H3N
OH
O

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

 Example 2.8.2
Acetic acid (CH3COOH) is known to have a pKa of 4.76. Please determine the Ka for acetic acid.

Solution
Solving for Ka algebraically you get the following:
pKa = -Log(Ka)
-pKa = Log(Ka)
10-pKa = Ka
Using a calculator first enter in the value for the pKa (4.76). The make the number negative (-4.76). Next, use the inverse log
function. All calculators are slightly different so this function may appear as: ANTILOG, INV LOG, or 10X. Often it is the
second function of the LOG button.
Ka for acetic acid = 10-pKa = 1.74 x 10-5

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

2.8.4 https://chem.libretexts.org/@go/page/31390
Answers
− + − +
[C H3 C O ][ H ] [C H3 C O ][ H3 O ]
1. Ka =
2
or K a =
2

[C H3 C O2 H ] [C H3 C O2 H ]

2. pK = − log K = 4.74 Thus, log K = − 4.72and K = anti-log(−4.72)= 1.9 × 10

a 10 a 10 a a
−5

3. pK = − log K = − log 6.5 × 10 = −(−4.19) = 4.19

a 10 a 10
−5

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

2.8: Acid and Base Strength is shared under a CC BY-SA 4.0 license and was authored, remixed, and/or curated by Tom Neils, Steven Farmer,
Dietmar Kennepohl, Krista Cunningham, Tim Soderberg, & Tim Soderberg.

2.8.5 https://chem.libretexts.org/@go/page/31390
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
use pKa values to 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:

O O H
C H + N H C
+
N H
H 3C O H 3C H Keq = ? H3C O H 3C H
pKa = 4.8 pKa = 10.6
(stronger 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
eq

had 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.

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 a) enz S + enz OH

H 3C O
b) + NH3
O

OH O
c) +

H H
d) N + OH

Answer

a) + enz OH + enz O
enz S enz SH

pKa ~ 17 pKa ~ 10

H 3C O Keq ~ 10−5 H 3C OH
b) + NH3 + NH2
O O
pKa ~ 10 pKa ~ 5

OH O O OH
Keq ~ 108
c) + +

pKa ~ 10 pKa ~ 18

H H Keq ~ 5 × 105 H
d) N + OH + H2O
N

pKa ~ 10 pKa ~ 15.7

4
The pKa of water is 14.0. Thus the Keq for reaction d) is ~ 10 .

Exercises

 Exercise 2.9.1

Use the pKa table from Section 2.8 and/or from the Reference Tables to determine if the following reactions would be
expected to occur:

a)

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 b)

c)

Answer
a) Yes - alkenes have pKa values of ~35 while alkynes have pKa values of ~25. This means that alkynes are more acidic and
more likely to donate a proton.
b) Yes - alkenes have pKa values of ~35 while alcohols have pKa values of ~16-18. This means that alcohols are more
acidic and more likely to donate a proton.
c) No - carboxylic acids have pKa values of ~4-5 while alcohols have pKa values of ~16-18. This means that carboxylic
acids are more acidic and more likely to donate a proton (so the reverse reaction would be expected to occur).

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

Solutions
S2.9.1

2.9: Predicting Acid-Base Reactions from pKa Values is shared under a CC BY-SA 4.0 license and was authored, remixed, and/or curated by
Steven Farmer, Dietmar Kennepohl, Layne Morsch, Krista Cunningham, Tim Soderberg, & Tim Soderberg.

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2.10: Organic Acids and Organic Bases
 Objective

After completing this section, you should be able to

predict the relative acidity of two organic molecules from their structures.
predict the relative basicity of two organic molecules from their structures.

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 ionized. The position of equilibrium therefore lies well to the left.

Weak acid polarization

Organic acids can usually can be characterized in electrostatic potential maps by the presence of of a positively polarized hydrogen
atom shown in blue. When looking at the maps below, methanol has a slightly polarized O-H bond and is considered very weakly
acidic. The O-H bond in methyl amine is less polarized, as shown by the lighter blue color around the hydrogen, making it less
acidic than methanol. However, the C-H bond in ethane lack virtually any polarity, as shown by the lack of a blue color, making it
non-acidic. The following discussion will explain the difference in acidity of these and other organic molecules molecules.

methanol methylamine ethane

Comparing the strengths of weak acids

Acid strength is strongly correlated to stability of the conjugate base that will form by removing a proton. In order to analyze how
acidic a molecule is likely to be, then you need to estimate the stability of its conjugate base.

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Stabilization of the Conjugate Base - Four Main Considerations:
1. Size and electronegativity of the atom holding the charge
2. Can the charge be delocalized by resonance?
3. Are there any inductive effects?
4. Hybridization of orbital holding the charge
These considerations are listed in order of importance and are explained individually, but must be looked at collectively.
1. Size and Electronegativity Effects in Acidity
When comparing elements, it depends on the positional relationship of the elements on the periodic table. When moving a period
(aka across a row) of the main group elements, the valence electrons all occupy orbitals in the same shell. These electrons have
comparable energy, so this factor does not help us discern differences relative stability. Differences in electronegativity are now the
dominant factor. This trend is shown when comparing the pKa values of ethane, methyl amine, and methanol which reflects the
relative electronegativities of the C < N < O. The key to understanding this trend is to consider the hypothetical conjugate base in
each case: the more stable the conjugate base, the stronger the acid. In general, the more electronegative an atom, the better it is
able to bear a negative charge. In the ethyl anion, the negative charge is borne by carbon, in the methylamine anion by nitrogen,
and in the methoxide anion by an oxygen. Remember the periodic trend in electronegativity: it also increases as we move from left
to right along a row, meaning that oxygen is the most electronegative of three elements being considered. This makes the negative
charge on the methoxide anion the most stable of the three conjugate bases and methanol the strongest of the three acids. Likewise,
carbon is the least electronegative making ethane the weakest of the three acids.

H3C CH3 H3C CH2 + H+

ethane ethyl
pKa = 50 anion

H
H3C N H3 C N + H+
H H
methylamine methylamine
pKa = 40 anion

H 3C O +
H 3C O H+
H
methanol methanol anion
pKa = 15.5 (methoxide)

Within a Group (aka down a column) As we move down the periodic table, the electrons are occupying higher energy subshells
creating a larger atomic size and volume. As the volume of an element increases, any negative charge present tends to become
more spread out which decreases electron density and increases stability. The figure below shows spheres representing the atoms of
the s and p blocks from the periodic table to scale, showing the two trends for the atomic radius.

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 Figure 2.10.1 : Atomic Radii Trends on the Periodic Table. Although there are some reversals in the trend (e.g., see Po in the
bottom row), atoms generally get smaller as you go across the periodic table and larger as you go down any one column. Numbers
are the radii in pm.
This relationship of atomic size and electron density is illustrated when we compare the relative acidities of methanol, CH3OH,
with methanethiol, CH3SH. The lower pKa value of 10.4 for methanethiol indicates that it is a stronger acid than methanol with a
pKa value of 15.5. It is important to remember that neither compound is considered an acid. These relationships become useful
when trying to deprotonate compounds to increase their chemical reactivity in non-aqueous reaction conditions.

H3 C O +
H3C O H+
H
methanol
pKa = 15.5

H 3C S +
H3C S H+
H
methanethiol
pKa = 10.4

The difference in size can easily be seen when looking at the electrostatic potential maps for methanol (Left) and methanethiol
(Right). The sulfur atom methanethiol is larger than the oxygen atom in methanol. The larger size of sulfur will be better able to
delocalize and stabilize the negative charge in its conjugate base metanethiolate.

2.

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 Resonance Effects in Acidity
This section will focus on how the resonance structures of different organic groups contributes to their relative acidity even though
the same element acts as the proton donor. When evaluating conjugate bases for the presence of resonance contributors, remember
to look for movable electrons (lone pairs and pi bonding electrons). Delocalizing electrons over two or more atoms spreads out the
electron density, increasing the stability of the conjugate base, and increasing the acidity of the corresponding acid. A classic
example compares the relative acidity of ethanol and acetic acid, but the conclusions we reach will be equally valid for all alcohol
and carboxylic acid groups. Despite the fact that they are both oxygen acids, the pKa values of ethanol and acetic acid are very
different.

O O
H3C C H3C C + H+
O H O
acetic acid acetate
pKa = 4.8 anion

H3CH2C O +
H3CH2C O H+
H
ethanol ethoxide
pKa = 16 anion

In both species, the negative charge on the conjugate base is held by an oxygen, so periodic trends cannot be invoked. For acetic
acid, however, there is a key difference: a resonance contributor can be drawn in which the negative charge is drawn on the second
oxygen of the group. The two resonance forms for the conjugate base are equal in energy, according to our ‘rules of resonance’
(Section 2.5). What this means is that the negative charge on the acetate ion is not located on one oxygen or the other: rather it is
shared between the two. Chemists use the term ‘delocalization of charge’ to describe this situation. In the ethoxide ion, by contrast,
the negative charge is ‘locked’ on the single oxygen. This stabilization leads to a markedly increased acidity.
The delocalization of charge by resonance has a very powerful effect on the reactivity of organic molecules, enough to account for
the difference of nearly 12 pKa units between ethanol and acetic acid (and remember, pKa is a log expression, so we are talking
about a difference of over 1012 between the acidity constants for the two molecules). The acetate ion is much more stable than the
ethoxide ion, due to the effects of resonance delocalization.
The effects of conjugation can be seen when comparing the electrostatic potential maps of ethanol and acetic acid. Conjugation
creates a greater polarization in the O-H bond in acetic acid as shown by its darker blue color.

H
O O
H H C H
H C C H O C
H
H H H

ethanol acetic acid

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Why is Phenol Acidic?
Compounds like alcohols and phenol which contain an -OH group attached to a hydrocarbon are very weak acids. Alcohols are so
weakly acidic that, for normal lab purposes, their acidity can be virtually ignored. However, phenol is sufficiently acidic for it to
have recognizably acidic properties - even if it is still a very weak acid. A hydrogen ion can break away from the -OH group and
transfer to a base. For example, in aqueous solution:
OH O
+ H2 O + H3 O

phenoxide
ion

Since phenol is a very weak acid, the position of equilibrium lies well to the left. However, phenol can lose a hydrogen ion because
the phenoxide ion (or phenolate ion - the two terms can be used interchangeably) formed is stabilized due to resonance. The
negative charge on the oxygen atom is delocalized around the ring since one of the lone pairs on the oxygen atom can be in a p
orbital and overlap with the pi electrons on the benzene ring.

OH OH OH OH
phenol modest stabilization

+ base

−H

O O O O
phenolate strong stabilization
anion

This overlap leads to a delocalization which extends from the ring out over the oxygen atom. As a result, the negative charge is no
longer entirely localized on the oxygen, but is spread out around the whole ion. Spreading the charge around makes the ion more
stable than it would be if all the charge remained on the oxygen. However, oxygen is the most electronegative element in the ion
and the delocalized electrons will be drawn towards it. That means that there will still be a lot of charge around the oxygen which
will tend to attract the hydrogen ion back again. That is why phenol is only a very weak acid.
This explains why phenol is a much stronger acid than cyclohexanol. As can be seen in the following energy diagram, resonance
stabilization is increased for the conjugate base of phenol vs. cyclohexanol after removal of a proton.

The resonance stabilization in these two cases is very different. An important principle of resonance is that charge separation
diminishes the importance of contributors to the resonance hybrid. The contributing structures to the phenol hybrid all suffer charge
separation, resulting in very modest stabilization of this compound. On the other hand, the phenolate anion is already charged, and
the canonical contributors act to disperse the charge, resulting in a substantial stabilization of this species. The conjugate bases of
simple alcohols are not stabilized by charge delocalization, so the acidity of these compounds is similar to that of water. An energy
diagram showing the effect of resonance on cyclohexanol and phenol acidities is shown on the right. Since the resonance
stabilization of the phenolate conjugate base is much greater than the stabilization of phenol itself, the acidity of phenol relative to
cyclohexanol is increased. Supporting evidence that the phenolate negative charge is delocalized on the ortho and para carbons of
the benzene ring comes from the influence of electron-withdrawing substituents at those sites.

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Acidity of hydrogen α (alpha) to carbonyl
Alkyl hydrogen atoms bonded to a carbon atom in a α (alpha) position (directly adjacent) relative to a C=O group display unusual
acidity. While the pKa values for alkyl C-H bonds in is typically on the order of 40-50, pKa values for these alpha hydrogens is
more on the order of 19-20. This is almost exclusively due to the resonance stabilization of the product carbanion, called an
enolate, as illustrated in the diagram below. The effect of the the stabilizing C=O is seen when comparing the pKa for the α
hydrogens of aldehydes (~16-18), ketones (~19-21), and esters (~23-25).

O O O
C H + base C R C R
R C R C R C
R
R R R

enolate ion

3. Inductive Effects
The inductive effect is an experimentally observed effect of the transmission of charge through a chain of atoms in a molecule,
resulting in a permanent dipole in a bond. For example, in a carboxylic acid group the presence of chlorine on adjacent carbons
increases the acidity of the carboxylic acid group. A chlorine atom is more electronegative than hydrogen, and thus is able to
‘induce’, or ‘pull’ electron density towards itself, away from the carboxylate group. This further spreads out the electron density of
the conjugate base, which has a stabilizing effect. In this context, the chlorine substituent is called an electron-withdrawing
group. Notice that the pKa-lowering effect of each chlorine atom, while significant, is not as dramatic as the delocalizing resonance
effect illustrated by the difference in pKa values between an alcohol and a carboxylic acid. In general, resonance effects are more
powerful than inductive effects.
O
Cl CH2 C
𝛅− 𝛅+
O

negative charge is delocalized by being pulled out onto chlorine atom

Compare the pKa values of acetic acid and its mono-, di-, and tri-chlorinated derivatives:
H O H H O Cl H O Cl H O Cl
O C C H O C C H O C C Cl O C C C
l
H H H Cl

pKa = 4.8 pKa = 2.8 pKa = 1.3 pKa = 0.64

The inductive effects of chlorine can be clearly seen when looking at the electrostatic potential maps of acetic acid (Left) and
trichloroacetic acid (Right). The O-H bond in trichloroacetic acid is highly polarized as shown by the dark blue color. This
illustrates that tricholoracetic acid is a much stronger acid than acetic acid.

O O

H C H H C Cl
O C O C
Cl Cl
H H

acetic acid trichloroacetic acid

Because the inductive effect depends on electronegativity, fluorine substituents have a more pronounced pKa-lowering effect than
chlorine substituents.

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 Cl O H F O H
Cl C C O F C C O
Cl F
trichloroacetic acid trifluoroacetic acid
pKa = 0.64 pKa = −0.25

In addition, the inductive takes place through covalent bonds, and its influence decreases markedly with distance – thus a chlorine
two carbons away from a carboxylic acid group has a decreased effect compared to a chlorine just one carbon away. 2-
chloropropanoic acid has a pKa of 2.8 while for 3-chloropropanoic acid, the pKa is 4.0.
H Cl O H Cl H O H
H C C C O H C C C O
H H H H
2-chloropropanoic acid 3-chloropropanoic acid
pKa = 2.8 pKa = 4.0
stronger acid

Alkyl groups (hydrocarbons) are weak inductive electron donators. In this case the inductive effect pushes electron density onto the
conjugate base, causing the electron density to become more concentrated and producing a destabilizing effect.

O
H3C C
𝛅+ 𝛅−
O
more negative charge pushed towards already negative end
The inductive effects of alkyl groups causes a significant variation in the acidities of different carboxylic acids. Notice that the
inductive effect drops off after the alkyl chain is about three carbons long.

pKa

HCOOH (Methanoic Acid or Formic Acid) 3.75

CH3COOH (Ethanoic Acid or Acetic Acid) 4.76

CH3CH2COOH (Propanoic Acid) 4.87

CH3CH2CH2COOH (Butanoic Acid) 4.82

4. Orbital Hybridization
The hybridization of an orbital affects its electronegativity. Within a shell, the s orbitals occupy the region closer to the nucleus
than the p orbitals. Therefore, the spherical s orbitals are more electronegative than the lobed p orbitals. The relative
electronegativity of hybridized orbitals is sp > sp2 > sp3 since the percentage of s-character is decreasing as more p-orbitals are
added to the hybrids. This trend indicates the sp hybridized orbitals are more stable with a negative charge than sp3 hybridized
orbitals. The table below shows how orbital hybridization influences relative acidity.

compound conjugate base hybridization s character pKa

H H H H
H C C H H C C sp3 25% 50 weakest acid
H H H H

H H H
C C C C sp2 33% 44 ↓
H H H H

NH3 NH2 36 ↓

H C C H H C C sp 50% 25 ↓

ROH RO 16 strongest acid

Comparing the Strengths of Weak Bases

Technically, organic bases are characterized by the presence of an atom with lone pair electrons. These lone pairs contain a high
electron density, which is shown red in the electrostatic potential maps, and can bond to H+. Below are the maps of methanol,

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methyl amine, and acetone. All three compounds can be protonated with a sufficiently strong acid. Note, that all three of these
compounds also have the ability to donate a proton when reacted with a strong enough base. Whether these compounds act as a
acid or base depends on the conditions.

H O
H N H
O H C H
C C
H C H H C H
H H H H H H

methylamine methanol acetone

It is common to compare basicity's quantitatively by using the pKa's of their conjugate acids rather than their pKb's. Since pKa +
pKb = 14, the higher the pKa the stronger the base, in contrast to the usual inverse relationship of pKa with acidity. Recall that
ammonia (NH3) acts as a base because the nitrogen atom has a lone pair of electrons that can accept a proton. The conjugate acid of
most simple alkyl amines have pKa's in the range 9.5 to 11.0, and their water solutions are basic (have a pH of 11 to 12, depending
on concentration). This can be illustrated by the reaction below where an amine removes a proton from water to form substituted
ammonium (e.g. NH4+) ions and hydroxide (OH−) ions:
R R H
N + H2O H N H + OH
R H

Amines are one of the only neutral functional groups which are considered basic. This is a direct consequence of the presence of
the unshared electron pair on the nitrogen. The unshared electron pair is less tightly held by the nitrogen of an amine than the
corresponding oxygen of an alcohol, which makes it more available to act as a base. As a specific example, methylamine reacts
with water to form the methylammonium ion and the OH− ion.
H 3C H H
N + H 2O H 3C N H + OH
H H

 Example: Ammonia

All of the have similarities to 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.

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 𝛅+
H
𝛅+
H H
N𝛅− + O H N H + OH
H H
H𝛅+ H

When looking at the table below, it is clear that the basicity of nitrogen containing compounds is greatly influenced by their
structures. The variance in the basicity of these compounds can mostly be explained by the effects of electron delocalization
discussed above.
Table 2.10.1: pKa of conjugate acids of a series of amines.

H H
NH2 NH2 NH2 O
NH N
Compound N H H N
N R NH2
H3C C N
H O2 N

pKa 11.0 10.7 10.7 9.3 5.2 4.6 1.0 0.0 -1.0 -10.0

Inductive Effects in Nitrogen Basicity

Alkylamines are more basic than ammonia since alkyl groups donate electrons to the more electronegative nitrogen. This inductive
effect makes the electron density on the alkylamine nitrogen greater than the nitrogen of ammonium. 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. Correspondingly, primary, secondary, and tertiary alkyl amines are more basic
than ammonia.
𝛅+
H
𝛅−
H 3C N
𝛅+
𝛅+
H

methyl group pushes electron density toward the nitrogen, making it more basic
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:
H H
H 3C N𝛅− H H 3C N H
𝛅+
H H
CH3 group
pushes electron
density toward
nitrogen

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.
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.

Compound pKa

NH3 9.3

CH3NH2 10.66

(CH3)2NH 10.74

(CH3)3N 9.81

2.10.9 https://chem.libretexts.org/@go/page/31392
Resonance Effects in Nitrogen Basicity
The resonance effect also explains why a nitrogen atom is basic when it is in an amine, but not significantly basic when it is part of
an amide group. While the lone pair of electrons in an amine nitrogen is localized in one place, the lone pair on an amide nitrogen
is delocalized by resonance. The lone pair is stabilized by resonance delocalization. Here’s another way to think about it: the lone
pair on an amide nitrogen is not available for bonding with a proton – these two electrons are too stable being part of the
delocalized pi-bonding system. The electrostatic potential map show the effect of resonance on the basicity of an amide. The map
shows that the electron density, shown in red, is almost completely shifted towards the oxygen. This greatly decreases the basicity
of the lone pair electrons on the nitrogen in an amide.

R NH2
O
amine
R NH2
pKa of conjugate acid ~ 11
amide
pKa of conjugate acid ~ −1

Aniline, the amine analog of phenol, is substantially less basic than an amine (as evidenced by the pKa of the conjugate acids).
NH2 NH2

cyclohexylamine aniline
pKa of conjugate acid ~ 10 pKa of conjugate acid ~ 5

We can use the same reasoning that we used when comparing the acidity of a phenol to that of an alcohol. In aniline, the lone pair
on the nitrogen atom is stabilized by resonance with the aromatic pi system, making it less available for bonding and thus less
basic.
NH2 NH2 NH2 NH2

lone pair is stabilized through resonance

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 hydronium ion - so that's constant - but the nature of the anion (the negative ion) varies markedly from case to
case.

Exercises

 Exercise 2.10.1

Select the more basic from each of the following pairs of compounds.

(a)

(b)

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 Answer

a) The lone pair of electrons on the amide nitrogen are less available to react with a proton.
(b) NaOH -- The hydroxide has a negative charge with three lone pairs of electrons that can react with a proton.

 Exercise 2.10.2

The 4-methylbenzylammonium ion has a pKa of 9.51, and the butylammonium ion has a pKa of 10.59. Which is more basic?
What's the pKb for each compound?

Answer
The butylammonium is more basic. Remember that pKa+pKb = 14. The pKb for butylammonium is 3.41, the pKb for 4-
methylbenzylammonium is 4.49.

Questions

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

Solutions

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

2.10: Organic Acids and Organic Bases is shared under a CC BY-SA 4.0 license and was authored, remixed, and/or curated by Jim Clark, Steven
Farmer, Dietmar Kennepohl, Layne Morsch, Krista Cunningham, & Krista Cunningham.

2.10.11 https://chem.libretexts.org/@go/page/31392
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.
3. identify an organic molecule or ion in a reaction as either an electrophile or nucleophile.

 Key Terms
Make certain that you can define, and use in context, the key terms below.
Lewis acid
Lewis base
Electrophile
Nucleophile

 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
H
C
H H

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).

Introduction to Lewis Acid-Base Theory

The Brønsted acid-base theory has been used throughout the history of acid and base chemistry. However, this theory is very
restrictive and focuses primarily on acids and bases acting as proton donors and acceptors. Sometimes conditions arise where the
theory doesn't necessarily fit, such as in solids and gases. In 1923, G.N. Lewis from UC Berkeley proposed an alternate theory to
describe acids and bases. His theory gave a generalized explanation of acids and bases based on structure and bonding. Through the
use of the Lewis definition of acids and bases, chemists are now able to predict a wider variety of acid-base reactions. Lewis'
theory used electrons instead of proton transfer and specifically stated that an acid is a species that accepts an electron pair while a
base donates an electron pair.
2+
Mg
O Mg
O
C C
R R R R

Example of Lewis base (oxygen atom from carbonyl) reacting with Lewis Acid (Mg2+ ion).
The reaction of a Lewis acid and a Lewis base will produce a coordinate covalent bond. A coordinate covalent bond is just a type
of covalent bond in which one reactant donates both electrons to form the bond. In this case the Lewis base donates its electrons to
form a bond to the Lewis acid. The resulting product is called an addition compound, or more commonly a complex. The electron-
pair flow from Lewis base to Lewis acid is shown using curved arrows much like those used for resonance structures in Section
2.5. Curved arrows always mean that an electron pair moves from the atom at the tail of the arrow to the atom at the head of the
arrow. In this case the lone pair on the Lewis base attacks the Lewis acid forming a bond. This new type of electron pair movement,
along with those described in Section 2.5 will be used throughout this text to describe electron flow during reactions.
Lewis Acid: a species that accepts an electron pair and will typically either have vacant orbitals or a polar bond involving
hydrogen such that it can donate H+ (which has an empty 1s orbital)
Lewis Base: a species that donates an electron pair and will have lone-pair electrons of pi bonding electrons.

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Lewis Acids
Neutral compounds of boron, aluminum, and the other Group 13 elements, (BF3, AlCl3), which possess only six valence electrons,
have a very strong tendency to gain an additional electron pair. Because these compounds are only surrounded by three electron
groups, they are sp2 hybridized, contained a vacant p orbital, and are potent Lewis acids. Trimethylamine's lone pair elections are
contained in an sp3 hybrid orbital making it a Lewis base. These two orbitals overlap, creating a covalent bond in a boron
trifluoride-trimethylamine complex. The movement of electrons during this interaction is show by by an arrow.
H 3C F F H3C F
+ B H3C N B F
N
H 3C CH3 F H3C F

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.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.
2+
Mg
O Mg
O
C C
R R R R

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. 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. For example, 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.

O
Ti O
O
O

CH3 CH3
N N
H 3C Ce CH3
N
H 3C CH3

Figure 2.11.1 : Although titanium has eight electrons in this molecule, titanium tetrakis(isopropoxide), it can accommodate up to
eighteen. It is a Lewis acid. The cerium atom in cerium tris(dimethylamide) comes from a similar part of the periodic table and is
also a Lewis acid.
For example, 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.
Cl
O
Ti TiCl4(THF) THF TiCl4(THF)2
+ Cl Cl
Cl
THF TiCl4

Figure 2.11.2 : A Lewis acid-base complex between tetrahydrofuran (THF) and titanium tetrachloride.

The Proton as a Common Lewis Acid

Perhaps the most common example of a Lewis acid is also the simplest. It is the hydrogen cation (H+) 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. A proton is a Lewis acid for a number 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 helium noble gas configuration.

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 B + H B H

B = base
Figure 2.11.3 : Proton reacting as a 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 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 making is still act as a Lewis Acid.
A acid-base reaction involving protons might better be expressed as:

H
O + H Cl + Cl
H H O
H H
Figure 2.11.4 : Proton transfer from one site to another.
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. Two specific movements of electrons are shown in the
reaction both of which are show by arrows. Lone pair electrons on oxygen attack the hydrogen to form an O-H bond in the product.
Also, the electrons of the H-Cl bond move to become a lone pair on chlorine as the H-Cl bond breaks. These two arrows together
are said to represent the mechanism of this acid-base reaction.

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 this makes oxygen and nitrogen compounds common Lewis bases. Lewis bases may be
anionic or neutral. The basic requirement is that they have a pair of electrons to donate.
NH2 OH O S

O O O O

H O NH2

Figure 2.11.5 : Some common organic examples of Lewis bases. Most oxygen, nitrogen and sulfur containing compounds can act
as Lewis Bases.

 Note 1: Ammonia

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

NH3 + A H3 N A

Ammonia donating to an electron acceptor or Lewis acid.

Not all compounds can act as a Lewis base. For example, methane, CH4, has all of its valence electrons in bonding pairs. These
bonding pairs are too stable to donate under normal conditions therefore methane is not a Lewis base. Neutral boron compounds
also have all electrons in bonding pairs. For example, borane, BH3 has no lone pairs; all its valence electrons are in bonds. Boron
compounds are not typically Lewis bases.
H H
B
H H H C H
H

no lone pairs to donate

Figure 2.11.6 : Carbon and boron compounds with all sigma bonds do not have lone pairs, and do not act as Lewis bases.

2.11.3 https://chem.libretexts.org/@go/page/31393
  Exercise 2.11.1
Which of the following compounds would you expect to be Lewis bases?
a) SiH4 b) AlH3 c) PH3 d) SH2 e) -SH

Answer
a) No, silicon has 4 valence electrons (like carbon) and all 4 are involved in sigma bonds
b) No, aluminum has 3 valence electrons and all 3 are involved in sigma bonds
c) Yes, phosphorus has 5 valence electrons, so there is one lone pair available
d) Yes, sulfur has 6 valence electrons, so there are two lone pairs available
e) Yes, this ion has 3 lone pairs available

Lewis Acid-Base Complexes

What happens when a Lewis base donates a pair of electrons to a Lewis acid? The electron pushing formalism (arrows) we have
been using to illustrate the behavior 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.

B + A B A
electron electron
donor acceptor
(Lewis base) (Lewis acid)

Figure 2.11.7 : Donation of electrons from a Lewis base to a Lewis acid.

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.

F H F
F
H N H +
B N B
H F F HH F

Figure 2.11.8 : 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. A
coordinate bond is any covalent bond that arose because one atom brought a pair of its electrons and donated them to another.
In organic chemistry terminology, 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 means electron-
loving.

 Exercise 2.11.2

For the following reaction, add curved arrows (electron pushing formalism) to indicate the electron flow.

Answer

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  Exercise 2.11.3

A Lewis acid-base complex is formed between THF (tetrahyrofuran) and borane, BH3.
a) Which compound is the Lewis acid? Which one is the Lewis base?
b) Which atom in the Lewis acid is the acidic site? Why?
c) Which atom in the Lewis base is the basic site? Why?
d) How many donors would be needed to satisfy the acidic site?
e) Show, using arrow notation, the reaction to form a Lewis acid-base complex.
f) 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.
g) Borane-THF complex is much less pyrophoric than borane. Why do you suppose that is so?
Add exercises text here.

Answer
a) Borane is the Lewis acid. THF has lone pair electrons so it is the Lewis base.
b) The Boron atom has an unfilled octet so it has an empty p orbital that can accept electrons.
c) The oxygen atom in THF has lone pair electrons contained in a sp3 hybridized orbital.
d) The boron in borane has six electrons around it so it would only need one lone pair donor to reach an octet.
e) Show, using arrow notation, the reaction to form a Lewis acid-base complex.

f) The Borane initially reacts with water in air.

g) After the Borane-THF complex is formed, the boron atom has a complete octet making it less reactive.

Exercises
Questions
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.

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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.

2.11: Acids and Bases - The Lewis Definition is shared under a CC BY-SA 4.0 license and was authored, remixed, and/or curated by Chris
Schaller, Steven Farmer, Dietmar Kennepohl, Layne Morsch, Tim Soderberg, & Tim Soderberg.

2.11.6 https://chem.libretexts.org/@go/page/31393
2.12: Noncovalent Interactions Between Molecules
 Objectives

After completing this section, you should be able to

1. identify the various intermolecular forces that may be at play in a given organic compound.
2. describe how intermolecular forces influence the physical properties, 3‑dimensional shape and structure of compounds.

 Key Terms
Make certain that you can define, and use in context, the key terms below.
dipole-dipole forces
London dispersion forces
hydrogen bond
intermolecular forces
noncovalent interaction
van der Waals forces

 Study Notes

Much of the material in this section should be familiar to you from your pre-requisite general chemistry course. Nonetheless,
this section is important, as it covers some of the fundamental factors that influence many physical and chemical properties.

Introduction
The properties of liquids are intermediate between those of gases and solids, but are more similar to solids. In contrast to
intramolecular forces, such as the covalent bonds that hold atoms together in molecules and polyatomic ions, intermolecular forces
hold molecules together in a liquid or solid. Intermolecular forces are generally much weaker than covalent bonds. For example, it
requires 927 kJ to overcome the intramolecular forces and break both O–H bonds in 1 mol of water, but it takes only about 41 kJ to
overcome the intermolecular attractions and convert 1 mol of liquid water to water vapor at 100°C. (Despite this seemingly low
value, the intermolecular forces in liquid water are among the strongest such forces known!) Given the large difference in the
strengths of intra- and intermolecular forces, changes between the solid, liquid, and gaseous states almost invariably occur for
molecular substances without breaking covalent bonds.

 Note
The properties of liquids are intermediate between those of gases and solids but are more similar to solids.

Intermolecular forces determine bulk properties such as the melting points of solids and the boiling points of liquids. Liquids boil
when the molecules have enough thermal energy to overcome the intermolecular attractive forces that hold them together, thereby
forming bubbles of vapor within the liquid. Similarly, solids melt when the molecules acquire enough thermal energy to overcome
the intermolecular forces that lock them into place in the solid.
Intermolecular forces are electrostatic in nature; that is, they arise from the interaction between positively and negatively charged
species. Like covalent and ionic bonds, intermolecular interactions are the sum of both attractive and repulsive components.
Because electrostatic interactions fall off rapidly with increasing distance between molecules, intermolecular interactions are most
important for solids and liquids, where the molecules are close together. These interactions become important for gases only at very
high pressures, where they are responsible for the observed deviations from the ideal gas law.
In this section, we explicitly consider three kinds of intermolecular interactions: dipole-dipole forces, dispersion forces, and
hydrogen bonds. These intermolecular interactions are also called van der Waals forces or noncovalent interactions. There are two
additional types of electrostatic interaction that you are already familiar with: the ion–ion interactions that are responsible for ionic
bonding and the ion–dipole interactions that occur when ionic substances dissolve in a polar substance such as water. These are less
common with organic molecules, so will not be described further in this section.

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Dipole–Dipole Interactions
Polar covalent bonds behave as if the bonded atoms have localized fractional charges that are equal but opposite (i.e., the two
bonded atoms generate a dipole). If the structure of a molecule is such that the individual bond dipoles do not cancel one another,
then the molecule has a net dipole moment. Molecules with net dipole moments tend to align themselves so that the positive end of
one dipole is near the negative end of another and vice versa, as shown in Figure 2.12.1 parts (a and b). Arrangements in which two
positive or two negative ends are adjacent (parts (c and d) in Figure 2.12.1) are higher energy as the similar charges would repel
one another. Hence dipole–dipole interactions, such as those in parts (a and b) in Figure 2.12.1, are attractive intermolecular
interactions, whereas those in part (c and d) are repulsive intermolecular interactions.

Figure 2.12.1 Attractive and Repulsive Dipole–Dipole Interactions. (a and b) Molecular orientations in which the positive end of
one dipole (δ+) is near the negative end of another (δ−) (and vice versa) produce attractive interactions. (c and d) Molecular
orientations that juxtapose the positive or negative ends of the dipoles on adjacent molecules produce repulsive interactions.
Because molecules in a liquid move freely and continuously, molecules always experience both attractive and repulsive dipole–
dipole interactions simultaneously, as shown in Figure 2.12.2. On average, however, the attractive interactions dominate.

Figure 2.12.2 Both Attractive and Repulsive Dipole–Dipole Interactions Occur in a Liquid Sample with Many Molecules
Chloromethane is an example of a polar molecule. An electrostatic potential map shows a high electron density (seen in red)
around the electronegative chlorine giving it a partial negative charge. The other end of the molecule has electron density pulled
away from it giving it a partial positive charge seen in blue. The positive and negative ends of different chloromethane molecules
are attracted to one another through this electrostatic interaction.
𝛅+ 𝛅− 𝛅+ 𝛅−

Cl

H C H
H

chloromethane
(μ = 1.87 D)
Because each end of a dipole possesses only a fraction of the charge of an electron, dipole–dipole interactions are substantially
weaker than the interactions between two ions, each of which has a charge of at least ±1, or between a dipole and an ion, in which
one of the species has at least a full positive or negative charge. In addition, the attractive interaction between dipoles falls off

2.12.2 https://chem.libretexts.org/@go/page/169747
much more rapidly with increasing distance than do ion–ion interactions. Recall that the attractive energy between two ions is
proportional to 1/r, where r is the distance between the ions. Doubling the distance (r → 2r) decreases the attractive energy by one-
half. In contrast, the energy of the interaction of two dipoles is proportional to 1/r6, so doubling the distance between the dipoles
decreases the strength of the interaction by 26, or 64-fold. Thus a substance such as HCl, which is partially held together by dipole–
dipole interactions, is a gas at room temperature and 1 atm pressure, whereas NaCl, which is held together by ionic interactions, is a
high-melting-point solid. Within a series of compounds of similar molar mass, the strength of the intermolecular interactions
increases as the dipole moment of the molecules increases, as shown in Table 2.12.1. Using what we learned about predicting
relative bond polarities from the electronegativities of the bonded atoms, we can make educated guesses about the relative boiling
points of similar molecules.
Table 2.12.1: Relationships between the Dipole Moment and the Boiling Point for Organic Compounds of Similar Molar Mass
Compound Molar Mass (g/mol) Dipole Moment (D) Boiling Point (K)

C3H6 (cyclopropane) 42 0 240

CH3OCH3 (dimethyl ether) 46 1.30 248

CH3CN (acetonitrile) 41 3.9 355

 Note

The attractive energy between two ions is proportional to 1/r, whereas the attractive energy between two dipoles is proportional
to 1/r6.

 Example 2.12.1

Arrange ethyl methyl ether (CH3OCH2CH3), 2-methylpropane [isobutane, (CH3)2CHCH3], and acetone (CH3COCH3) in order
of increasing boiling points. Their structures are as follows:

Strategy:
Compare the molar masses and the polarities of the compounds. Compounds with higher molar masses and that are polar will have
the highest boiling points.
Solution:
The three compounds have essentially the same molar mass (58–60 g/mol), so we must look at differences in polarity to predict the
strength of the intermolecular dipole–dipole interactions and thus the boiling points of the compounds. The first compound, 2-
methylpropane, contains only C–H bonds, which are not very polar because C and H have similar electronegativity values. It
should therefore have a very small (but nonzero) dipole moment and a very low boiling point. Ethyl methyl ether has a structure
similar to H2O; it contains two polar C–O single bonds oriented at about a 109° angle to each other, in addition to relatively
nonpolar C–H bonds. As a result, the C–O bond dipoles partially reinforce one another and generate a significant dipole moment
that should give a moderately high boiling point. Acetone contains a polar C=O double bond oriented at about 120° to two methyl
groups with nonpolar C–H bonds. The C–O bond dipole therefore corresponds to the molecular dipole, which should result in both
a rather large dipole moment and a high boiling point. Thus we predict the following order of boiling points: 2-methylpropane <
ethyl methyl ether < acetone. This result is in good agreement with the actual data: 2-methylpropane, boiling point = −11.7°C, and
the dipole moment (μ) = 0.13 D; methyl ethyl ether, boiling point = 7.4°C and μ = 1.17 D; acetone, boiling point = 56.1°C and μ =
2.88 D.

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  Exercise 2.12.1
Arrange carbon tetrafluoride (CF4), ethyl methyl sulfide (CH3SC2H5), dimethyl sulfoxide [(CH3)2S=O], and 2-methylbutane
[isopentane, (CH3)2CHCH2CH3] in order of decreasing boiling points.

Answer
dimethyl sulfoxide (boiling point = 189.9°C) > ethyl methyl sulfide (boiling point = 67°C) > 2-methylbutane (boiling point
= 27.8°C) > carbon tetrafluoride (boiling point = −128°C)

London Dispersion Forces

Thus far we have considered only interactions between polar molecules, but other factors must be considered to explain why many
nonpolar molecules, such as bromine, benzene, and hexane, are liquids at room temperature, and others, such as iodine and
naphthalene, are solids. Even the noble gases can be liquefied or solidified at low temperatures, high pressures, or both.
What kind of attractive forces can exist between nonpolar molecules or atoms? This question was answered by Fritz London
(1900–1954), a German physicist who later worked in the United States. In 1930, London proposed that temporary fluctuations in
the electron distributions within atoms and nonpolar molecules could result in the formation of short-lived instantaneous dipole
moments, which produce attractive forces called London dispersion forces between otherwise nonpolar substances.
Table 2.12.2: Normal Melting and Boiling Points of Some Elements and Nonpolar Compounds
Substance Molar Mass (g/mol) Melting Point (°C) Boiling Point (°C)

Ar 40 −189.4 −185.9

Xe 131 −111.8 −108.1

N2 28 −210 −195.8

O2 32 −218.8 −183.0

F2 38 −219.7 −188.1

I2 254 113.7 184.4

CH4 16 −182.5 −161.5

Consider a pair of adjacent He atoms, for example. On average, the two electrons in each He atom are uniformly distributed around
the nucleus. Because the electrons are in constant motion, however, their distribution in one atom is likely to be asymmetrical at
any given instant, resulting in an instantaneous dipole moment. As shown in part (a) in Figure 2.12.3, the instantaneous dipole
moment on one atom can interact with the electrons in an adjacent atom, pulling them toward the positive end of the instantaneous
dipole or repelling them from the negative end. The net effect is that the first atom causes the temporary formation of a dipole,
called an induced dipole, in the second. Interactions between these temporary dipoles cause atoms to be attracted to one another.
These attractive interactions are weak and fall off rapidly with increasing distance. London was able to show with quantum
mechanics that the attractive energy between molecules due to temporary dipole–induced dipole interactions falls off as 1/r6.
Doubling the distance therefore decreases the attractive energy by 26, or 64-fold.

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 Figure 2.12.3 Instantaneous Dipole Moments. The formation of an instantaneous dipole moment on one He atom (a) or an H2
molecule (b) results in the formation of an induced dipole on an adjacent atom or molecule.
Instantaneous dipole–induced dipole interactions between nonpolar molecules can produce intermolecular attractions just as they
produce interatomic attractions in monatomic substances like Xe. This effect, illustrated for two H2 molecules in part (b) in Figure
2.12.3, tends to become more pronounced as atomic and molecular masses increase (Table 2.12.3). For example, Xe boils at
−108.1°C, whereas He boils at −269°C. The reason for this trend is that the strength of London dispersion forces is related to the
ease with which the electron distribution in a given atom can be perturbed. In small atoms such as He, the two 1s electrons are held
close to the nucleus in a very small volume, and electron–electron repulsions are strong enough to prevent significant asymmetry in
their distribution. In larger atoms such as Xe, however, the outer electrons are much less strongly attracted to the nucleus because
of filled intervening shells. As a result, it is relatively easy to temporarily deform the electron distribution to generate an
instantaneous or induced dipole. The ease of deformation of the electron distribution in an atom or molecule is called its
polarizability. Because the electron distribution is more easily perturbed in large, heavy species than in small, light species, we say
that heavier substances tend to be much more polarizable than lighter ones.

 Note

For similar substances, London dispersion forces get stronger with increasing molecular size.

The polarizability of a substance also determines how it interacts with ions and species that possess permanent dipoles. Thus
London dispersion forces are responsible for the general trend toward higher boiling points with increased molecular mass and
greater surface area in a homologous series of compounds, such as the alkanes (part (a) in Figure 2.12.4). The strengths of London
dispersion forces also depend significantly on molecular shape because shape determines how much of one molecule can interact
with its neighboring molecules at any given time. For example, part (b) in Figure 2.12.4 shows 2,2-dimethylpropane (neopentane)
and n-pentane, both of which have the empirical formula C5H12. Neopentane is almost spherical, with a small surface area for
intermolecular interactions, whereas n-pentane has an extended conformation that enables it to come into close contact with other
n-pentane molecules. As a result, the boiling point of neopentane (9.5°C) is more than 25°C lower than the boiling point of n-
pentane (36.1°C).

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 Figure 2.12.4 Mass and Surface Area Affect the Strength of London Dispersion Forces. (a) In this series of four simple alkanes,
larger molecules have stronger London forces between them than smaller molecules and consequently higher boiling points. (b)
Linear n-pentane molecules have a larger surface area and stronger intermolecular forces than spherical neopentane molecules. As
a result, neopentane is a gas at room temperature, whereas n-pentane is a volatile liquid.
All molecules, whether polar or nonpolar, are attracted to one another by London dispersion forces in addition to any other
attractive forces that may be present. In general, however, dipole–dipole interactions in small polar molecules are significantly
stronger than London dispersion forces, so the former predominate.

 Example 2.12.2

Arrange n-butane, propane, 2-methylpropane [isobutane], and n-pentane in order of increasing boiling points.
Strategy:
Determine the intermolecular forces in the compounds and then arrange the compounds according to the strength of those
forces. The substance with the weakest forces will have the lowest boiling point.
Solution:
The four compounds are alkanes and nonpolar, so London dispersion forces are the only important intermolecular forces.
These forces are generally stronger with increasing molecular mass, so propane should have the lowest boiling point and n-
pentane should have the highest, with the two butane isomers falling in between. Of the two butane isomers, 2-methylpropane
is more compact, and n-butane has the more extended shape. Consequently, we expect intermolecular interactions for n-butane
to be stronger due to its larger surface area, resulting in a higher boiling point. The overall order is thus as follows, with actual
boiling points in parentheses: propane (−42.1°C) < 2-methylpropane (−11.7°C) < n-butane (−0.5°C) < n-pentane (36.1°C).

 Exercise 2.12.2
Arrange GeH4, SiCl4, SiH4, CH4, and GeCl4 in order of decreasing boiling points.

Answer
GeCl4 (87°C) > SiCl4 (57.6°C) > GeH4 (−88.5°C) > SiH4 (−111.8°C) > CH4 (−161°C)

Hydrogen Bonds
Molecules with hydrogen atoms bonded to electronegative atoms such as O, N, and F (and to a much lesser extent Cl and S) tend to
exhibit unusually strong intermolecular interactions. These result in much higher boiling points than are observed for substances in
which London dispersion forces dominate, as illustrated for the covalent hydrides of elements of groups 14–17 in Figure 2.12.5.
Methane and its heavier congeners in group 14 form a series whose boiling points increase smoothly with increasing molar mass.
This is the expected trend in nonpolar molecules, for which London dispersion forces are the exclusive intermolecular forces. In
contrast, the hydrides of the lightest members of groups 15–17 have boiling points that are more than 100°C greater than predicted

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on the basis of their molar masses. The effect is most dramatic for water: if we extend the straight line connecting the points for
H2Te and H2Se to the line for period 2, we obtain an estimated boiling point of −130°C for water! Imagine the implications for life
on Earth if water boiled at −130°C rather than 100°C.

Figure 2.12.5: The Effects of Hydrogen Bonding on Boiling Points. These plots of the boiling points of the covalent hydrides of the
elements of groups 14–17 show that the boiling points of the lightest members of each series for which hydrogen bonding is
possible (HF, NH3, and H2O) are anomalously high for compounds with such low molecular masses.
Why do strong intermolecular forces produce such anomalously high boiling points and other unusual properties, such as high
enthalpies of vaporization and high melting points? The answer lies in the highly polar nature of the bonds between hydrogen and
very electronegative elements such as O, N, and F. The large difference in electronegativity results in a large partial positive charge
on hydrogen and a correspondingly large partial negative charge on the O, N, or F atom. Consequently, H–O, H–N, and H–F bonds
have very large bond dipoles that can interact strongly with one another. Because a hydrogen atom is so small, these dipoles can
also approach one another more closely than most other dipoles. The combination of large bond dipoles and short dipole–dipole
distances results in very strong dipole–dipole interactions called hydrogen bonds, as shown for ice in Figure 2.12.6.
A hydrogen bond is usually indicated by a dotted line between the hydrogen atom attached to O, N, or F (the hydrogen bond donor)
and the atom that has the lone pair of electrons (the hydrogen bond acceptor). Because each water molecule contains two hydrogen
atoms and two lone pairs, a tetrahedral arrangement maximizes the number of hydrogen bonds that can be formed. In the structure
of ice, each oxygen atom is surrounded by a distorted tetrahedron of hydrogen atoms that form bridges to the oxygen atoms of
adjacent water molecules. The bridging hydrogen atoms are not equidistant from the two oxygen atoms they connect, however.
Instead, each hydrogen atom is 101 pm from one oxygen and 174 pm from the other. In contrast, each oxygen atom is bonded to
two H atoms at the shorter distance and two at the longer distance, corresponding to two O–H covalent bonds and two O⋅⋅⋅H
hydrogen bonds from adjacent water molecules, respectively. The resulting open, cagelike structure of ice means that the solid is
actually slightly less dense than the liquid, which explains why ice floats on water rather than sinks.

Figure 2.12.6: The Hydrogen-Bonded Structure of Ice

Each water molecule accepts two hydrogen bonds from two other water molecules and donates two hydrogen atoms to form
hydrogen bonds with two more water molecules, producing an open, cage-like structure. The structure of liquid water is very
similar, but in the liquid, the hydrogen bonds are continually broken and formed because of rapid molecular motion.

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  Note
Hydrogen bond formation requires both a hydrogen bond donor and a hydrogen bond acceptor.

Because ice is less dense than liquid water, rivers, lakes, and oceans freeze from the top down. In fact, the ice forms a protective
surface layer that insulates the rest of the water, allowing fish and other organisms to survive in the lower levels of a frozen lake or
sea. If ice were denser than the liquid, the ice formed at the surface in cold weather would sink as fast as it formed. Bodies of water
would freeze from the bottom up, which would be lethal for most aquatic creatures. The expansion of water when freezing also
explains why automobile or boat engines must be protected by “antifreeze” and why unprotected pipes in houses break if they are
allowed to freeze.
Although hydrogen bonds are significantly weaker than covalent bonds, with typical dissociation energies of only 15–25 kJ/mol,
they have a significant influence on the physical properties of a compound. Compounds such as HF can form only two hydrogen
bonds at a time as can, on average, pure liquid NH3. Consequently, even though their molecular masses are similar to that of water,
their boiling points are significantly lower than the boiling point of water, which forms four hydrogen bonds at a time.

 Example 2.12.3
Considering CH3OH, C2H6, Xe, and (CH3)3N, which can form hydrogen bonds with themselves? Draw the hydrogen-bonded
structures.
Strategy:
A. Identify the compounds with a hydrogen atom attached to O, N, or F. These are likely to be able to act as hydrogen bond
donors.
B. Of the compounds that can act as hydrogen bond donors, identify those that also contain lone pairs of electrons, which
allow them to be hydrogen bond acceptors. If a substance is both a hydrogen donor and a hydrogen bond acceptor, draw a
structure showing the hydrogen bonding.
Solution:
A Of the species listed, xenon (Xe), ethane (C2H6), and trimethylamine [(CH3)3N] do not contain a hydrogen atom attached to
O, N, or F; hence they cannot act as hydrogen bond donors.
B The one compound that can act as a hydrogen bond donor, methanol (CH3OH), contains both a hydrogen atom attached to O
(making it a hydrogen bond donor) and two lone pairs of electrons on O (making it a hydrogen bond acceptor); methanol can
thus form hydrogen bonds by acting as either a hydrogen bond donor or a hydrogen bond acceptor. The hydrogen-bonded
structure of methanol is as follows:
lone pair

O hydrogen bond
H 3C H

O
H CH3

O
H 3C H

 Exercise 2.12.3
Considering CH3CO2H, (CH3)3N, NH3, and CH3F, which can form hydrogen bonds with themselves? Draw the hydrogen-
bonded structures.
Answer: CH3CO2H and NH3;
H H
H N H N H
H
HH O H O H
C C C C
N H
H O H O HH HH

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  Example 2.12.4
Arrange C60 (buckminsterfullerene, which has a cage structure), NaCl, He, Ar, and N2O in order of increasing boiling points.
Given: compounds
Asked for: order of increasing boiling points
Strategy:
Identify the intermolecular forces in each compound and then arrange the compounds according to the strength of those forces.
The substance with the weakest forces will have the lowest boiling point.
Solution:
Electrostatic interactions are strongest for an ionic compound, so we expect NaCl to have the highest boiling point. To predict
the relative boiling points of the other compounds, we must consider their polarity (for dipole–dipole interactions), their ability
to form hydrogen bonds, and their molar mass (for London dispersion forces). Helium is nonpolar and by far the lightest, so it
should have the lowest boiling point. Argon and N2O have very similar molar masses (40 and 44 g/mol, respectively), but N2O
is polar while Ar is not. Consequently, N2O should have a higher boiling point. A C60 molecule is nonpolar, but its molar mass
is 720 g/mol, much greater than that of Ar or N2O. Because the boiling points of nonpolar substances increase rapidly with
molecular mass, C60 should boil at a higher temperature than the other nonionic substances. The predicted order is thus as
follows, with actual boiling points in parentheses: He (−269°C) < Ar (−185.7°C) < N2O (−88.5°C) < C60 (>280°C) < NaCl
(1465°C).

 Exercise 2.12.4

Arrange 2,4-dimethylheptane, Ne, CS2, Cl2, and KBr in order of decreasing boiling points.
Answer: KBr (1435°C) > 2,4-dimethylheptane (132.9°C) > CS2 (46.6°C) > Cl2 (−34.6°C) > Ne (−246°C)

Summary
Molecules in liquids are held to other molecules by intermolecular interactions, which are weaker than the intramolecular
interactions that hold the atoms together within molecules and polyatomic ions. Transitions between the solid and liquid or the
liquid and gas phases are due to changes in intermolecular interactions but do not affect intramolecular interactions. The three
major types of intermolecular interactions are dipole–dipole interactions, London dispersion forces (these two are often referred to
collectively as van der Waals forces), and hydrogen bonds. Dipole–dipole interactions arise from the electrostatic interactions of
the positive and negative ends of molecules with permanent dipole moments; their strength is proportional to the magnitude of the
dipole moment and to 1/r6, where r is the distance between dipoles. London dispersion forces are due to the formation of
instantaneous dipole moments in polar or nonpolar molecules as a result of short-lived fluctuations of electron charge
distribution, which in turn cause the temporary formation of an induced dipole in adjacent molecules. Like dipole–dipole
interactions, their energy falls off as 1/r6. Larger atoms tend to be more polarizable than smaller ones because their outer electrons
are less tightly bound and are therefore more easily perturbed. Hydrogen bonds are especially strong dipole–dipole interactions
between molecules that have hydrogen bonded to a highly electronegative atom, such as O, N, or F. The resulting partially
positively charged H atom on one molecule (the hydrogen bond donor) can interact strongly with a lone pair of electrons of a
partially negatively charged O, N, or F atom on adjacent molecules (the hydrogen bond acceptor). Because of strong
O ⋅ ⋅ ⋅ H hydrogen bonding between water molecules, water has an unusually high boiling point, and ice has an open, cagelike

structure that is less dense than liquid water.

Key Takeaway
Intermolecular forces are electrostatic in nature and include van der Waals forces and hydrogen bonds.

Problems
1. Which are stronger—dipole–dipole interactions or London dispersion forces? Which are likely to be more important in a
molecule with heavy atoms? Explain your answers.

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 2. Liquid water is essential for life as we know it, but based on its molecular mass, water should be a gas under standard
conditions. Why is water a liquid rather than a gas under standard conditions?
3. Why are intermolecular interactions more important for liquids and solids than for gases? Under what conditions must these
interactions be considered for gases?
4. In group 17, elemental fluorine and chlorine are gases, whereas bromine is a liquid and iodine is a solid. Why?
5. Identify the most important intermolecular interaction in each of the following.
a) SO2
b) HF
c) CO2
d) CCl4
e) CH2Cl2
6. Both water and methanol have anomalously high boiling points due to hydrogen bonding, but the boiling point of water is
greater than that of methanol despite its lower molecular mass. Why? Draw the structures of these two compounds, including
any lone pairs, and indicate potential hydrogen bonds.
7. Do you expect the boiling point of H2S to be higher or lower than that of H2O? Justify your answer.
8. Some recipes call for vigorous boiling, while others call for gentle simmering. What is the difference in the temperature of the
cooking liquid between boiling and simmering? What is the difference in energy input?

Solutions
1. Dipole-Diple interactions are stronger because molecules polarity is permanent. Molecules involved in London dispersion forces
are only temporarily polar
2. Water is a liquid under standard conditions because of its unique ability to form four strong hydrogen bonds per molecule.
3. In solids and liquids the molecules are in direct contact. In gases the molecules only contact during collisions. Intermolecules
forces become inmportant when gases are cooled to the point where they form a liquid. 4. As the atomic mass of the halogens
increases, so does the number of electrons and the average distance of those electrons from the nucleus. Larger atoms with more
electrons are more easily polarized than smaller atoms, and the increase in polarizability with atomic number increases the strength
of London dispersion forces. These intermolecular interactions are strong enough to favor the condensed states for bromine and
iodine under normal conditions of temperature and pressure. 5. a) The V-shaped SO2 molecule has a large dipole moment due to
the polar S=O bonds, so dipole–dipole interactions will be most important.
b) The H–F bond is highly polar, and the fluorine atom has three lone pairs of electrons to act as hydrogen bond acceptors;
hydrogen bonding will be most important.
c) Although the C=O bonds are polar, this linear molecule has no net dipole moment; hence, London dispersion forces are most
important.
d) This is a symmetrical molecule that has no net dipole moment, and the Cl atoms are relatively polarizable; thus, London
dispersion forces will dominate.
e) This molecule has a small dipole moment, as well as polarizable Cl atoms. In such a case, dipole–dipole interactions and London
dispersion forces are often comparable in magnitude.
6) Water has two polar O–H bonds with H atoms that can act as hydrogen bond donors, plus two lone pairs of electrons that can act
as hydrogen bond acceptors, giving a net of four hydrogen bonds per H2O molecule. Although methanol also has two lone pairs of
electrons on oxygen that can act as hydrogen bond acceptors, it only has one O–H bond with an H atom that can act as a hydrogen
bond donor. Consequently, methanol can only form two hydrogen bonds per molecule on average, versus four for water. Hydrogen
bonding therefore has a much greater effect on the boiling point of water.
7) H2O would have the higher boiling point because it can form the stronger hydrogen bonding intermolecular force. 8) Vigorous
boiling causes more water molecule to escape into the vapor phase, but does not affect the temperature of the liquid. Vigorous
boiling requires a higher energy input than does gentle simmering.

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2.12: Noncovalent Interactions Between Molecules is shared under a CC BY-SA 4.0 license and was authored, remixed, and/or curated by Steven
Farmer, Dietmar Kennepohl, Krista Cunningham, Tim Soderberg, William Reusch, Mark Perri, & Mark Perri.

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2.MM: 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 by their common names, which may be more familiar than their IUPAC
counterparts. We shall address the subject of nomenclature (naming) in Chapter 3.
ethanol ethanol

formaldehyde (methanal),

acetone (propanone),

acetic (ethanoic) acid,

If your instructor is having you work with molecular models in class, they may use this section for you to practice creating specific
structures.

Exercises
1. Construct a molecular model of each of the compounds listed below.
a. $\ce{\sf{CH3-CN}}$
b. $\ce{\sf{CH3-N=C=O}}$
c. $\ce{\sf{CH3-CH2-O-CH3}}$
Hint: Use the curved sticks to form the multiple bonds and the straight sticks for single bonds.

Answers:
A.

B.

C.

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2.MM: Molecular Models is shared under a CC BY-SA 4.0 license and was authored, remixed, and/or curated by Steven Farmer & Dietmar
Kennepohl.

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2.S: Polar Covalent Bonds; Acids and Bases (Summary)
Concepts & Vocabulary
2.1 Polar Covalent Bonds: Electronegativity
The difference in electronegativity values of two atoms determines whether the bond between those atoms is classified as either
ionic, polar covalent, or non-polar covalent.
Ionic bonds result from large differences in electronegativity values, such as that between a metal and non-metal atom (Na and
Cl).
Covalent bonding generally results when both atoms are non-metals, like C, H, O, N and the halides.
When both atoms the same and/or have the same electronegativity value, then the bonding electrons are shared equally and the
bond is classified as non-polar covalent.
Polar covalent bonds occur when the difference in electronegativity values is small, and the bonding electrons are not shared
equally.
2.2 Polar Covalent Bonds: Dipole Moments
The molecular dipole moment is the sum of all the bond dipoles within a molecule and depends on both the molecular
geometry and the bond polarity.
Molecules that contain no polar bonds, like CH4, and/or completely symmetrical molecules, like CO2, generally have no net
dipole moment.
Asymmetrical molecules that contain bonds of different polarities or non-bonding lone pairs typically have a molecular dipole
moment.
2.3 Formal Charges
Formal Charge compares how many valence electrons surround a free atom versus how many surround that same type of atom
bonded with a molecule or ion.
Formal Charge = (# of valence electrons in free atom) - (# of lone-pair electrons) - (1/2 # of bond pair electrons) Eqn.
2.3.1
Formal charges of zero generally represent the most stable structures.
These bonding patterns for the atoms commonly found in organic molecules result in a formal charge of zero
Carbon - 4 bonds, no lone pairs
Hydrogen - 1 bond, no lone pairs
Nitrogen - 3 bonds, 1 lone pair
Oxygen - 2 bonds, 2 lone pairs
Halogens - 1 bond, 3 lone pairs.
2.4 Resonance
Resonance Theory is often used when the observed chemical and physical properties of a molecule or ion cannot be adequately
described by a single Lewis Structure. A classic example is the benzene molecule, C6H6. The Lewis Structure of benzene could
be drawn in two different ways. Both structures have alternating double bond and single bonds between the carbons. The only

difference is the location of the pi bonds.

If these structures are correct, then the benzene molecule should have two different C-C bond lengths and bond energies,
corresponding to a C-C single bond and to a C=C double bond. However, analysis shows that benzene contains only one type of
carbon-carbon bond and it's bond length and energy are half between those of a single bond and double bond. Resonance theory
states that benzene exists as the "average" of the two structures called a resonance hybrid, in which the six pi electrons
delocalized over all six carbon atoms. Each C-C bond in benzene would be the average of a single bond and double bond or a

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"bond and a half". Dashed lines are often used to show type of "partial" bonding in a resonance hybrid of benzene

2.5 Rules for Resonance Forms

The rules for estimating stability of resonance structures are
The resonance form in which all atoms have complete valence shells is more stable.
The greater the number of covalent bonds, the greater the stability since more atoms will have complete octets
The structure with the least number of formal charges is more stable
The structure with the least separation of formal charges is more stable
A structure with a negative charge on the more electronegative atom will be more stable
Positive charges on the least electronegative atom (most electropositive) is more stable
Resonance forms that are equivalent have no difference in stability and contribute equally. (eg. benzene)
If these rules are applied to the two Lewis Structures of benzene, the result would be that both structures will have the same
relative stability and will both contribute equally to the character of the resonance hybrid.

2.6 Drawing Resonance Forms

In resonance structures, the electrons are able to move to help stabilize the molecule. This movement of the electrons is called
delocalization.
The rules for drawing resonance structures are:
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)
All resonance structures must follow the rules of writing Lewis Structures.
The hybridization of the structure must stay the same.
The skeleton of the structure can not be changed (only the electrons move).
Resonance structures must also have the same amount of lone pairs.
2.7 Acids and Bases - The Brønsted-Lowry Definition
A Brønsted-Lowry acid is a proton (H+) donor and a Brønsted-Lowry base is a proton acceptor.
2.8 Acid and Base Strength
The strength of Brønsted-Lowry acids is measured indicated by its pKa value. The lower the pKa - the stronger the acid.
A strong acid will have a weak conjugate base. A strong base will have a weak conjugate acid.
2.9 Predicting Acid-Base Reactions from pKa Values
The equilibrium of an acid-base reaction favors the formation of weaker acids from stronger acids. To predict the direction of
the equilibrium, identify Brønsted-Lowry acid on each side of the reaction. Assign/look up pKa values for each acid. The
equilibrium will favor the side that has the weakest acid (the highest pKa).
2.10 Organic Acids and Organic Bases
Organic acids are stronger when the conjugate base that is formed upon loss of a proton is more stable.
Some factors that effect the stability of the conjugate base (often an anion) are the anionic atom's size and electronegativity,
resonance effects, inductive effects, and solvation.
2.11: Acids and Bases - The Lewis Definition
A Lewis acid is a lone pair acceptor and a Lewis base is a lone pair donor.

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2.12: Non-covalent Interactions between Molecules
Non-covalent Interactions, also known as Intermolecular Forces, significantly effect the physical properties of organic
molecules. Hydrogen bonding is the most important of these interactions, but others include ion-dipole, dipole-dipole, and
London Dispersion Forces.
2.MM: Molecular Models

Summary Problems

 Exercise 2.S. 1

Draw all possible resonance structures to demonstrate delocalization of the positive charge in the following molecule. Circle
the most stable resonance structure and explain your answer. Also, draw the resonance hybrid.

Answer

N N

O O

N N

O O

N N

O O

N N

O O

Most stable resonance structure

d d d

N
d

d O
d
Resonance Hybrid

The circled structure is the most stable because it is the only structure with a full octet on all atoms. (Remember that
carbocations must have an incomplete octet, and an oxygen with a positive charge and a full octet is more stable than a
carbocation.)

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 As a reminder, the resonance hybrid structure is a combination of all of your resonance structure showing partial pi bonds
and partial formal charges.

 Exercise 2.S. 2

Draw all possible resonance structures to demonstrate delocalization of the negative charge in the following molecule. Also,
draw the resonance hybrid and circle the most stable resonance contributor among all of your resonance structures.
O

Answer
O O

N N

O O

N N

Most stable resonance structure

d
O
d
d

d
N

Resonance Hybrid

The circled structure is the most stable because the negative charge is on oxygen, the most electronegative element sharing
the negative charge. As a reminder, in resonance structures with negative charges, all of the atoms have octets, so you only
need to focus on electronegativity differences to find the most stable structure.

 Exercise 2.S. 3

For the equilibrium shown below, answer the following questions: a) Draw curved arrows to illustrate bond breakage and
formation in the reaction. b) At equilibrium, are the products or reactants favored? Explain. c) What percent reactants and
percent products are present at equilibrium? d) Use resonance structures to explain why N is the most basic atom in the
conjugate base. e) Use resonance structures to explain why the hydrogen that is removed from the conjugate acid is the most
acidic proton.

H O O O O O O
O N S O N S
+ +

pKa = 12.5
pKa = 17.5

Answer
a)

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 H O O O O O O
O N S O N S
+ +

pKa = 12.5
pKa = 17.5

b) The lower pKa is the stronger acid, and the equilibrium will always favor the weak acid (higher pKa), so this reaction
favors the reactants. Note: It's normal to assume that the neutral products would be favored, but this is a good example that
shows our chemical intuition isn't always right. To make sure we understand the equilibrium, we need to have pKa values
to compare.
c) Keq = 1012.5-17.5 = 10-5 = 0.00001 So, the ratio of reactants to products is 1:0.00001. The percent reactants is 99.999%
and the percent products is 0.001%.
d) There are two atoms with lone pairs in the conjugate base, O and N, so we should evaluate both to show that N is the
most basic atom. Protonating O yields a positive charge localized on O. Protonating N yields a charge delocalized over 3
Cs, 1 N, and 1 O. The N is most basic because the charge in the acid is delocalized and there are two structures with full
octets (positive charge on N and O).
H+ H
O N Protonate O O N
Localized
Charge

Conjugate Base

H+
Protonate N

H H H
O N O N O N

Delocalized
Charge

H H
O N O N

e) To find the most acidic proton, we should focus on Hs on atoms next to (not on) double bonds. This will yield a
delocalized negative charge when the H is removed. In the conjugate acid, we have two options. Option 1 yields a
compound with a negative charge delocalized over 2 atoms, O and C. Option 2 yields the base from the original reaction
because the charge is delocalized over 4 atoms, C and 3 Os. This is very stable because it is spread over 3 electronegative
oxygen atoms.

O O O O O O O O O
S H charge
Base S S
delocalized
Option 1 over 2 atoms
H

Option 2 Base

O O O O O O
S S

charge
delocalized
over 4 atoms

O O O O O O
S S

 Exercise 2.S. 4

This question focuses on the reaction of the two molecules shown below. a) Draw an acid-base reaction of these molecules.
Clearly label the acid, the base, the conjugate acid, and the conjugate base. Draw curved arrows to clearly indicate electron
movement involved in bond formation and bond cleavage. For the base and the conjugate base, label the hybridization of the
charged atoms. b) If you drew the reaction correctly, the pKa of the conjugate acid is 9. Use the table in Section 2.8 to

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determine the pKa of the acid. Are the reactants or products favored at equilibrium? What is the approximate ratio of reactants
to products? What is the approximate percentage of reactants and products? c) Draw the structures of the two charged
molecules in the reaction. Draw resonance structures to illustrate charge delocalization in these molecules. Based on your
analysis in part b, which charged molecule is more stable? Briefly explain this result.
OH O O
+

Answer
a)
sp2 hybridized
sp2 hybridized
O O O O O O
H
+ +

Acid Base Conjugate Conjugate

Base Acid

Don't forget that the charged atoms in the base and conjugate base are sp2 hybridized so that the lone pair can be in a p
orbital and then delocalized by resonance. For negative charges to be delocalized, the lone pair must be in a p orbital so that
electrons can flow to adjacent pi bonds by resonance.
b)
O O O O O O
H
+ +

pKa = 9.9 pKa = 9

The acid has the larger pKa, so it is the weaker acid and the reactants are favored. The approximate difference in pKa
values is 1. So, Keq is 10-1 and for every 1 product molecule there are 10 reactant molecules. (Remember, since the
reactants are favored, there are more reactants and the Keq must be less than 1.) The approximate percentage of reactants is
90% and products is 10%. (10/(10+1) is approximately 90% and 1/(10+1) is approximately 10%)
c)
charge delocalized
O O O O O O over 3 atoms

Base

O O O O
charge delocalized
over 4 atoms

Conjugate
Base

We know that the equilibrium favors the reactants. We also know that in acid base reactions, the stronger acid reacts with
the stronger base to yield the weaker base and the weaker acid. In this reaction, the products are the stronger acid-base pair.
We also know that "stronger" means more reactive and less stable, while "weaker" means less reactive and more stable. So,
since the reactants are favored, that means the base (as labeled above) is more stable than the conjugate base. This seems
strange since the charge is more delocalized in the conjugate base. This comparison highlights the importance of quality of
resonance structures versus quantity of resonance structures. The charge is more stable in the base since in two of the
resonance structures, the negative charge is on O. In the conjugate base, only one of the structures has the negative charge
on O.

 Exercise 2.S. 5
Determine the position of the most acidic proton in the following molecule. You should draw resonance structures and a
resonance hybrid to justify your answer.

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 O H

Answer
Donation of the most acidic proton (H+) yields the most stable conjugate base; the one that has the charge on the most
electronegative element and/or the most delocalized charge. You should focus on protons attached to electronegative
elements (e.g., O or N) and protons on atoms next to pi bonds, but not attached to atoms with pi bonds. In this molecule, all
Hs are attached to carbon. So, we should focus on the Hs next to pi bonds. These are Hs on sp3 hybridized carbons next to
sp2 hybridized carbons. Loss of these protons will yield a negative charge that can be delocalized by resonance.
O H O H O H

Option #1 Delocalized
over 2 atoms
Base (C and O)
H
H
O O O

Option #2 Base

O H O H d
O H

Delocalized d
over 5 atoms
(3C and 2O)
d
d
O O O
d
Hybrid

O H O H O H

O O O

Option #1 yields a conjugate base with the charge delocalized over 1 carbon and 1 oxygen. Option #2 yields a conjugate
base with a charge delocalized over 3 carbons and 2 oxygens. This is the most stable conjugate base, so the most acidic
proton is the red proton (removed in option #2).

 Exercise 2.S. 6

Determine the position of the most basic atom in the following molecule. You should draw resonance structures and a
resonance hybrid to justify your answer.

O N O

Answer
There are four basic atoms (atoms with lone pair electrons) in this molecule. The strongest base will yield the most stable
conjugate acid (the one with the most delocalized positive charge and/or the charge on the least electronegative atom).

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 Option #1
localized charge O N O H

Option #2
localized charge
O N O
H
O

Option #3
charge delocalized O O O
over 3 atoms H N O H N O H N O
(C, O, N)
O O O

Option #4
charge delocalized O N O O O
N
over 4 atoms
(C, N, 2O)
O O
H H

O d O O O
N O d N N O
d
O O O
H H H
d
Hybrid

O N O

Most Basic Atom

Options #1 and #2 yield conjugate acids with localized charges. Options #3 and #4 yield conjugate acids with delocalized
charges.This illustrates a key point: For atoms that can't have an expanded octet, atoms with a lone pair and no pi bond will
accept a proton and yield a localized charge in the conjugate acid while atoms with both a lone pair and a pi bond will
accept a proton and yield a delocalized charge in the conjugate acid. So, we should focus our energy on the latter atoms. In
this problem, that means Options #3 and #4. In option #3, the charge is delocalized over 3 atoms, 2 that have full octets on
all atoms (positive charge on N and O). In option #4, the charge is delocalized over 4 atoms, 3 that have full octets on all
atoms (positive charge on N and 2 Os). So, Option #4 has more total resonance structures and more structures that have a
full octet. This is the most stable conjugate acid which means the circled O is the most basic atom.

Skills to Master
Skill 2.1 Predict whether a bond is ionic, polar covalent, or non-polar covalent based on the position of the atoms in the periodic
table.
Skill 2.2 Identify the partial positive and partial negative atoms of a polar covalent bond based on relative electronegativity.
Skill 2.3 Determine the dipole moment of a molecule based on molecular geometry and bond polarity.
Skill 2.4 Identify the chemicals in a reaction as Brønsted-Lowry acids or bases, and conjugate acids and bases.
Skill 2.5 Predict the products of an acid-base reaction.

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 Skill 2.6 Use pKa values to predict the equilibrium direction of an acid-base reaction.
Skill 2.7 Predict the relative strength of an organic acid by examining the stability of the conjugate base.
Skill 2.8 Use molecular structure and analysis of intermolecular forces to rank a series of organic molecules with respect to
physical properties like melting point and boiling point.
Skill 2.9 Identify the chemicals in a reaction as Lewis acids or bases.

Memorization Tasks (MT)

MT 2.1 Memorize that the C-H bond is considered to be non-polar.
MT 2.2 Memorize the common bonding patterns for C, H, N, O and the halogens that have a zero formal charge.
MT 2.3 Memorize the factors that affect the relativity stability of conjugate bases.

2.S: Polar Covalent Bonds; Acids and Bases (Summary) is shared under a CC BY-SA 4.0 license and was authored, remixed, and/or curated by
Kelly Matthews & Kevin M. Shea.

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 CHAPTER OVERVIEW
3: Organic Compounds- Alkanes and Their Stereochemistry
 Learning 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.

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: Functional Groups
3.2: Alkanes and Alkane Isomers
3.3: Alkyl Groups
3.4: Naming Alkanes
3.5: Properties of Alkanes
3.6: Conformations of Ethane
3.7: Conformations of Other Alkanes
3.8: Gasoline - A Deeper Look
3.S: Organic Compounds- Alkanes and Their Stereochemistry (Summary)

3: Organic Compounds- Alkanes and Their Stereochemistry is shared under a CC BY-SA 4.0 license and was authored, remixed, and/or curated
by Dietmar Kennepohl.

1
3.1: 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 small groups of atoms that exhibit a characteristic reactivity. A particular functional group will almost
always display its distinctive chemical behavior when it is present in a compound. Because of their importance in understanding
organic chemistry, functional groups have specific names that often carry over in the naming of individual compounds
incorporating the 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.

Drawing abbreviated organic structures

Often when drawing organic structures, chemists find it convenient to use the letter 'R' to designate part of a molecule outside of
the region of interest. If we just want to refer in general to a functional group without drawing a specific molecule, for example, we
can use 'R groups' to focus attention on the group of interest:
H H O O
R C OH R C OH C C
H R H R R R

a primary a secondary an aldehyde a ketone

alcohol alcohol

The 'R' group is a convenient way to abbreviate the structures of large biological molecules, especially when we are interested in
something that is occurring specifically at one location on the molecule.

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Common Functional Groups
In the following sections, many of the common functional groups found in organic chemistry will be described. Tables of these
functional groups can be found at the bottom of the page.

Hydrocarbons
The simplest functional group in organic chemistry (which is often ignored when listing functional groups) is called an alkane,
characterized by single bonds between two carbons and between carbon and hydrogen. Some examples of alkanes include methane,
CH4, is the natural gas you may burn in your furnace or on a stove. Octane, C8H18, is a component of gasoline.
Alkanes
H H H H H H H H
H C C C C C C C C H
H H H H H H H H H
H C H

=
H

methane

octane

Alkenes (sometimes called olefins) have carbon-carbon double bonds, and alkynes have carbon-carbon triple bonds. Ethene, the
simplest alkene example, is a gas that serves as a cellular signal in fruits to stimulate ripening. (If you want bananas to ripen
quickly, put them in a paper bag along with an apple - the apple emits ethene gas, setting off the ripening process in the bananas).
Ethyne, commonly called acetylene, is used as a fuel in welding blow torches.
Alkenes and alkynes
H H
C C H C C H
H H
ethene ethyne
(an alkene) (an alkyne)

Alkenes have trigonal planar electron geometry (due to sp2 hybrid orbitals at the alkene carbons) while alkynes have linear
geometry (due to sp hybrid orbitals at the alkyne carbons). Furthermore, many alkenes can take two geometric forms: cis or trans
(or Z and E which will be explained in detail in Chapter 7). The cis and trans forms of a given alkene are different molecules with
different physical properties there is a very high energy barrier to rotation about a double bond. In the example below, the
difference between cis and trans alkenes is readily apparent.
H 3C CH3 H 3C H
C C C C
H H H CH3

cis -alkene trans -alkene

CH3 groups on CH3 groups on
the same side opposite sides

Alkanes, alkenes, and alkynes are all classified as hydrocarbons, because they are composed solely of carbon and hydrogen atoms.
Alkanes are said to be saturated hydrocarbons, because the carbons are bonded to the maximum possible number of hydrogens -
in other words, they are saturated with hydrogen atoms. The double and triple-bonded carbons in alkenes and alkynes have fewer
hydrogen atoms bonded to them - they are thus referred to as unsaturated hydrocarbons. As we will see in Chapter 7, hydrogen
can be added to double and triple bonds, in a type of reaction called 'hydrogenation'.
The aromatic group is exemplified by benzene (which used to be a commonly used solvent on the organic lab, but which was
shown to be carcinogenic), and naphthalene, a compound with a distinctive 'mothball' smell. Aromatic groups are planar (flat) ring
structures, and are widespread in nature. We will learn more about the structure and reactions of aromatic groups in Chapter 15.

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 Aromatics
H
H C H
C C
=
C C
H C H
H
benzene naphthalene

Functional Groups with Carbon Single Bonds to other Atoms

Halides
When the carbon of an alkane is bonded to one or more halogens, the group is referred to as a alkyl halide or haloalkane. The
presence of a halogen atom (F, Cl, Br, or I), is often represented by X due to the similar chemistry of halogens. Chloroform is a
useful solvent in the laboratory, and was one of the earlier anesthetic drugs used in surgery. Chlorodifluoromethane was used as a
refrigerant and in aerosol sprays until the late twentieth century, but its use was discontinued after it was found to have harmful
effects on the ozone layer. Bromoethane is a simple alkyl halide often used in organic synthesis. Alkyl halides groups are quite rare
in biomolecules.
H Cl H H
Cl C Cl F C Cl H C C Br
Cl F H H

trichloromethane dichlorodifluoromethane bromoethane

(chloroform) (Freon-12)

Alcohols and Thiols

In the alcohol functional group, a carbon is single-bonded to an OH group (the OH group, by itself, is referred to as a hydroxyl).
Except for methanol, all alcohols can be classified as primary, secondary, or tertiary. In a primary alcohol, the carbon bonded to
the OH group is also bonded to only one other carbon. In a secondary alcohol and tertiary alcohol, the carbon is bonded to two or
three other carbons, respectively. When the hydroxyl group is directly attached to an aromatic ring, the resulting group is called a
phenol.
H
H H H CH3 H C OH
C C
H C OH H3C C OH H3C C OH H3C C OH
C C
H H CH3 CH3 H C H

methanol a primary a secondary a tertiary H

alcohol alcohol alcohol a phenol

The sulfur analog of an alcohol is called a thiol (the prefix thio, derived from the Greek, refers to sulfur).
H H CH3
H 3C C SH H 3C C SH H 3C C SH
H CH3 CH3

a primary a secondary a tertiary

thiol thiol thiol

Ethers and sulfides

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.
H H H H
O H C C O C C H
H H H H

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

S
S

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Amines
Amines are characterized by nitrogen atoms with single bonds to hydrogen and carbon. Just as there are primary, secondary, and
tertiary alcohols, there are primary, secondary, and tertiary amines. Ammonia is a special case with no carbon atoms.

H N H H N CH3 H N CH3 H3 C N CH3

H H CH3 CH3

ammonia a primary a secondary a tertiary

amine amine amine

One of the most important properties of amines is that they are basic, and are readily protonated to form ammonium cations. In the
case where a nitrogen has four bonds to carbon (which is somewhat unusual in biomolecules), it is called a quaternary ammonium
ion.

H N H H N CH3 H N CH3 H3 C N CH3

H H CH3 CH3

ammonia a primary a secondary a tertiary

amine amine amine

H H CH3
H N H H N CH3 H 3C N CH3
H H CH3
ammonium a primary a quaternary
ion ammonium ion ammonium ion

 Caution

Do not be confused by how the terms 'primary', 'secondary', and 'tertiary' are applied to alcohols and amines - the definitions
are different. In alcohols, what matters is how many other carbons the alcohol carbon is bonded to, while in amines, what
matters is how many carbons the nitrogen is bonded to.

carbon is bonded to nitrogen is bonded to

three carbons one carbon

CH3
H 3C C OH H N CH3

CH3 H

a tertiary a primary
alcohol amine

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.
O O O
C C C
H H H CH3 H3C CH3

formaldehyde an aldehyde a ketone

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.

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 O O
C C
H OH H 3C OH

formic acid acetic acid

(vinegar)

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 Chapter 20).
O O
C C
H O H 3C O

formate acetate

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.
O O O
C H C CH3 C CH3
H3C N H3C N H 3C N
H H CH3

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.
O O
C CH3 C CH3
H 3C O H 3C S

an ester a thioester

In an acid anhydride, there are two carbonyl carbons with an oxygen in between. An acid anhydride is formed from combination
of two carboxylic acids with the loss of water (anhydride).
O O
C C
H3C O CH3

an anhydride

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.
O
O O
C
H 3C O P O C
H3C Cl
O
an acyl an acid
phosphate chloride

Nitriles and Imines

In a nitrile group, a carbon is triple-bonded to a nitrogen. Nitriles are also often referred to as cyano groups.
H 3C C N

a nitrile

Molecules with carbon-nitrogen double bonds are called imines, or Schiff bases.
H CH3
N N
C C
H3 C CH3 H3 C CH3

imines

Phosphates
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.

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 O
O O O
O P O O
O P O P O
O OH O P O
O O
O

inorganic an organic an organic

phosphate phosphate ester diphosphate ester

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.
O O

O
=
OH O P O OH OP
O

O O
O P O P O = PPO
O O

Molecules with Multiple Functional Groups

A single compound may contain several different 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’).
OH OH O OH OH OH

H
OH OH OH OH OH O

glucose fructose

Capsaicin, the compound responsible for the heat in hot peppers, contains phenol, ether, amide, and alkene functional groups.
HO
H
N
O
O
capsaicin

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

OH O OH

O CH3

O
acetylsalicylic acid
testosterone (aspirin)

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 found below provides a summary of all of the groups listed in this section,
plus a few more that will be introduced later in the text.

 Exercise 3.1.1

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

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 Answer
a) carboxylate, sulfide, aromatic, two amide groups (one of which is cyclic)
b) tertiary alcohol, thioester
c) carboxylate, ketone
d) ether, primary amine, alkene

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.

Functional Group Tables

Exclusively Carbon Functional Groups
Group Formula Class Name Specific Example IUPAC Name Common Name

C C alkene H2C=CH2 ethene ethylene

C C alkyne HC≡CH ethyne acetylene

arene C6H6 benzene benzene

Functional Groups with Single Bonds to Heteroatoms

Group Formula Class Name Specific Example IUPAC Name Common Name

C X halide H3C-I iodomethane methyl iodide

C OH alcohol CH3CH2OH ethanol ethyl alcohol

C O C ether CH3CH2OCH2CH3 diethyl ether ether

C N
amine H3C-NH2 aminomethane methylamine

O
C N
O
nitro compound H3C-NO2 nitromethane

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 Group Formula Class Name Specific Example IUPAC Name Common Name

C SH thiol H3C-SH methanethiol methyl mercaptan

C S C sulfide H3C-S-CH3 dimethyl sulfide

Functional Groups with Multiple Bonds to Heteroatoms

Group Formula Class Name Specific Example IUPAC Name Common Name

C C N nitrile H3C-CN ethanenitrile acetonitrile

O
C C aldehyde H3CCHO ethanal acetaldehyde
H

O
C C ketone H3CCOCH3 propanone acetone
C

O
C C carboxylic acid H3CCO2H ethanoic Acid acetic acid
OH

O
C C
O C
ester H3CCO2CH2CH3 ethyl ethanoate ethyl acetate

O
C C
X
acid halide H3CCOCl ethanoyl chloride acetyl chloride

O
C C
N
amide H3CCON(CH3)2 N,N-dimethylethanamide N,N-dimethylacetamide

O
C C O
O C acid Anhydride (H3CCO)2O ethanoic anhydride acetic anhydride
C

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

3.1.8 https://chem.libretexts.org/@go/page/31398
3.1: Functional Groups is shared under a CC BY-SA 4.0 license and was authored, remixed, and/or curated by Steven Farmer, Dietmar
Kennepohl, Layne Morsch, Krista Cunningham, Tim Soderberg, & Tim Soderberg.

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3.2: 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 are often called saturated hydrocarbons because they have the maximum possible number of hydrogens per
carbon. In Section 1.7, thealkane molecule, ethane, was shown to contain a C-C sigma bond. By adding more C-C sigma bond
larger and more complexed alkanes can be formed. Methane (CH4), ethane (C2H6), and propane (C3H8) are the beginning of a
series of compounds in which any two members in a sequence differ by one carbon atom and two hydrogen atoms—namely, a CH2
unit. Any family of compounds in which adjacent members differ from each other by a definite factor (here a CH2 group) is called
a homologous series. The members of such a series, called homologs, have properties that vary in a regular and predictable manner.
H H H H H H
H C H H C C H H C C C H
H H H H H H

methane ethane propane

Figure 25.3.1 : The Three Simplest Alkanes

Methane (CH4), ethane (C2H6), and propane (C3H8) are the beginning of a series of compounds in which any two members in a
sequence differ by one carbon atom and two hydrogen atoms—namely, a CH2 unit. Consider the series in Figure 25.3.3. The
sequence starts with C3H8, and a CH2 unit is added in each step moving up the series. Any family of compounds in which adjacent

3.2.1 https://chem.libretexts.org/@go/page/31399
members differ from each other by a definite factor (here a CH2 group) is called a homologous series. The members of such a
series, called homologs, have properties that vary in a regular and predictable manner.
H H H H
H C C C C H
H H H H
butane

H H H H H H H H H H H
H C C C C C H H C C C C C C H
H H H H H H H H H H H

pentane hexane

Figure 25.3.2: Members of a Homologous Series. Each succeeding formula incorporates one carbon atom and two hydrogen atoms
more than the previous formula.
The homologous series allows us to write a general formula for alkanes: CnH2n + 2. Using this formula, we can write a molecular
formula for any alkane with a given number of carbon atoms. For example, an alkane with eight carbon atoms has the molecular
formula C8H(2 × 8) + 2 = C8H18.

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:
Table 3.2.1 : Molecular formulas for small alkanes

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
All of the alkanes containing 4 or more carbon atoms show structural isomerism, meaning that there are two or more different
structural formulas that you can draw for each molecular formula. Isomers (from the Greek isos + meros, meaning "made of the
same parts") are molecules that have the same molecular formula, but have a different arrangement of the atoms in space. Alkanes
with 1-3 carbons, methane (CH4), ethane (C2H6), and propane (C3H8,) do not exist in isomeric forms because there is only one way
to arrange the atoms in each formula so that each carbon atom has four bonds. However, C4H10, has more than possible structure.
The four carbons can be drawn in a row to form butane or the can branch to form isobutane. The two compounds have different
properties—for example, butane boils at −0.5°C, while isobutane boils at −11.7°C.
H H H
H H H H
H C C C H
H C C C C H
H C H
H H H H H H
H
butane isobutane

Likewise the molecular formula: C5H12 has three possible isomer. The compound at the far left is pentane because it has all five
carbon atoms in a continuous chain. The compound in the middle is isopentane; like isobutane, it has a one CH3 branch off the
second carbon atom of the continuous chain. The compound at the far right, discovered after the other two, was named neopentane
(from the Greek neos, meaning “new”). Although all three have the same molecular formula, they have different properties,
including boiling points: pentane, 36.1°C; isopentane, 27.7°C; and neopentane, 9.5°C.

3.2.2 https://chem.libretexts.org/@go/page/31399
 H
H H H H H H
H H H H H H C H
H C C C C H
H C C C C C H H C C C H
H C H H
H H H H H H H H C H
H H H
H
pentane isopentane neopentane

Of the structures show above, butane and pentane are called normal alkanes or straight-chain alkanes, indicating that all contain
a single continuous chain of carbon atoms and can be represented by a projection formula whose carbon atoms are in a straight line.
The other structures, isobutane, isopentane, and neopentane are called called branched-chain alkanes. As the number of carbons in
an akane increases the number of possible isomers also increases as shown in the table below.
Table 3.2.2 : Number of isomers for hydrocarbons

Molecular Formula Number of Structural Isomers

CH4 1

C2H6 1

C3H8 1

C4H10 2

C5H12 3

C6H14 5

C7H16 9

C8H18 18

C9H20 35

C10H22 75

C14H30 1858

C18H38 60,523

C30H62 4,111,846,763

Akanes can be represented in many different ways. The figure below shows some of the different ways straight-chain butane can be
represented. Most often chemists refer to butane by the condensed structure CH3CH2CH2CH3 or n-C4H10 where n denotes a normal
straight alkane.
C4H10 CH3CH2CH2CH3

H H H H
H2
H C C C C H H3 C C C CH3
H2
H H H H

H H H
H
H C C
C C H
H
H H H

Note that many of these structures only imply bonding connections and do not indicate any particular geometry. The bottom two
structures, referred to as "ball and stick" and "space filling" do show 3D geometry for butane. Because the four-carbon chain in
butane may be bent in various ways the groups can rotate freely about the C–C bonds. However, this rotation does not change the
identity of the compound. It is important to realize that bending a chain does not change the identity of the compound; all of the
following represent the same compound, butane:

3.2.3 https://chem.libretexts.org/@go/page/31399
 CH3 H2
H2 H3 C C C CH3
H3C C CH2 H2

H 3C
CH3 CH3
H 2C CH2
H2C CH2
CH3

The nomenclature of straight alkanes is based on the number of carbon atoms they contain. The number of carbons are indicated by
a prefix and the suffix -ane is added to indicate the molecules is an alkane. The prefix for three carbons is prop so adding -ane, the
IUPAC name for C3H8 is propane. Likewise, the prefix for six is hex so the name for the straight chain isomer of C6H14 is called
hexane. The first ten prefixes should be memorized, because these alkane names from the basis for naming many other organic
compounds.
9.2.1" role="presentation" style="position:relative;" tabindex="0">
Table 3.2.3 : The First 10 Straight-Chain Alkanes
Molecular Formula Prefix Condensed Structural Formula Name

CH4 Meth CH4 methane

C2H6 Eth CH3CH3 ethane

C3H8 Prop CH3CH2CH3 propane

C4H10 But CH3CH2CH2CH3 butane

C5H12 Pent CH3CH2CH2CH2CH3 pentane

C6H14 Hex CH3(CH2)4CH3 hexane

C7H16 Hept CH3(CH2)5CH3 heptane

C8H18 Oct CH3(CH2)6CH3 octane

C9H20 Non CH3(CH2)7CH3 nonane

C10H22 Dec CH3(CH2)8CH3 decane

 Example 3.2.1: 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.
CH3
CH3 CH2 CH2 CH2 CH2 CH3
CH3 CH2 CH CH3

CH3
CH3 C CH3
CH3

Exercises

 Exercise 3.2.1
Draw all of the isomers for C6H14O that contain a 6 carbon chain and an alcohol (-OH) functional group.

Answer
OH
HO
OH

3.2.4 https://chem.libretexts.org/@go/page/31399
 Exercise 3.2.2

Draw all possible isomers for C6H14 (There are five total).

Answer

The top structure is when it is a 6 carbon chain. The middle row contains the 5 carbon chained isomers with branching at
the 2nd and 3rd carbon. The bottom row contains the two 4 carbon chain isomers that can be drawn.

 Exercise 3.2.3

Draw all possible isomers for C3H8.

Answer
The first structure is when an alcohol comes off the first carbon. The second structure is when the alcohol is coming off the
central carbon. The third structure is the only possible ether form of C3H8.
OH
O
HO

 Exercise 3.2.4

Draw all possible isomers for C4H8O2 that contain a carboxylic acid.

Answer
There are only 2 possibilities.
O
O
HO
HO

 Exercise 3.2.5

Draw all possible isomers for C3H9N and indicate whether each amine is primary, secondary, or tertiary.

Answer
NH2 H
NH2 N N

The first and second structures are primary amines. The third structure is a secondary amine. The last structure is a tertiary
amine.

3.2.5 https://chem.libretexts.org/@go/page/31399
  Exercise 3.2.6

Indicate whether each of the following sets are constitutional isomers, the same compound, or different compounds.
a)

&

b)
CH3
& CH3CH2CCH2CH3
CH3

c)
&

d) &

Answer
a) Both structures have formulas of C10H22 and have different connectivity which makes these constitutional isomers.
b) Both structures have formulas of C7H16 and have the same connectivity which makes these the same compound.
c) Both structure have formulas of C7H16 and have different connectivity which makes these constitutional isomers.
d) The structure on the left has a formula of C9H20 and the structure on the right has a formula of C10H22 so these are
different compounds.

 Exercise 3.2.7
Draw the 5 constitutional isomers of C7H16 (of the 9 total isomers possible) that have 5 carbons as the longest carbon chain
length.

Answer

The 5 constitutional isomers with a 5 carbon chain length are shown above. Since there needs to be 7 carbons total, the 2
extra carbons are added as substituents. From left to right, the methyl group substitution pattern is 2,2, 2,3, 2,4, and 3,3, and
the last one (on right) has a 3-ethyl substituent.
The other 4 possible constitutional isomers (with different length carbon chains) are shown below.

3.2: Alkanes and Alkane Isomers is shared under a CC BY-SA 4.0 license and was authored, remixed, and/or curated by Steven Farmer, Dietmar
Kennepohl, Zachary Sharrett, Layne Morsch, Krista Cunningham, Tim Soderberg, & Tim Soderberg.

3.2.6 https://chem.libretexts.org/@go/page/31399
3.3: 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
isopropyl group
sec-butyl group
isobutyl group
tert-butyl group
primary carbon
secondary carbon
tertiary carbon
quaternary 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 and second, that we have names for simple
alkyl groups that may be attached to the chains. An alkyl group is formed by removing one hydrogen from the alkane chain. The
removal of this hydrogen results in a stem change from -ane to -yl to indicate an alkyl group. The removal of a hydrogen from
methane, CH4, creates a methyl group -CH3. Likewise, the removal of a hydrogen from ethane, CH3CH3, creates an ethyl group -
CH2CH3. The nomenclature pattern can continue to provide a series of straight-chain alkyl groups from straight chain alkanes with
a hydrogen removed from the end. Note, the letter R is used to designate a generic (unspecified) alkyl group.
CH4 CH3 R
methane methyl

CH3CH2CH3 CH3CH2CH2 R
propane propyl

Table 3.3.2 : Straight chain alkane and alkyl group names

Alkane Name Alkyl Group Name (Abbreviation)

CH4 Methane -CH3 Methyl (Me)

CH3CH3 Ethane -CH2CH3 Ethyl (Et)

CH3CH2CH3 Propane -CH2CH2CH3 Propyl (Pr)

CH3CH2CH2CH3 Butane -CH2CH2CH2CH3 Butyl (Bu)

CH3CH2CH2CH2CH3 Pentane -CH2CH2CH2CH2CH3 Pentyl

3.3.1 https://chem.libretexts.org/@go/page/31400
 Alkane Name Alkyl Group Name (Abbreviation)

CH3CH2CH2CH2CH2CH3 Hexane -CH2CH2CH2CH2CH2CH3 Hexyl

Prior to the systematic nomenclature developed for organic chemistry, prefixes were used to specify the connection point of
straight-chain and branched-chain alkyl groups. Although the modern nomenclature system, discussed in the next section, is
preferred these older terms are still often used, especially in solvents and reagents. Thus, an understanding of these prefixes is
important to understanding organic chemistry. Notice that the total number of carbons in the alkyl subsistent is still indicated with
the prefix + yl. For methyl and ethyl alkyl groups there is only one possible connection point so connection prefixes are not
necessary. Starting with a three carbon alkyl group (propyl) the possibility of multiple connection points necessitates connection
prefixes. These prefixes are often abbreviated with a letter which is italicized.

Normal (n)
The prefix "n" is used to indicate a connection at the end of a straight-chain alkane. This prefix is not commonly used to just
indicate alkyl subsistent as discussed above. However it is sometime used to indicate the connection of a functional group onto a
straight alkane.
H2 H2 H2 H2 H2
C CH3 C C C C CH3
C C CH3 C C
H2 H2 H2 H2
n-propyl n-butyl n-pentyl
or propyl or butyl or pentyl

Iso (i)
Starting with propyl alkyl groups there is the possibility of a connection other than the very end. The prefix "iso" implies that the
connection ends with a (CH3)2CH- group.
H3C H3C H3C
H C H C CH2 H C CH2 CH2
H3C H3C H3C

isopropyl isobutyl isopentyl

or i-propyl or i-butyl or i-pentyl

Secondary (Sec)
With butyl straight-chain alkyl groups there is the possibility of a connection on the second carbon from the end of the chain. These
alkyl groups are given the prefix "Sec." This is not used for pentyl or hexyl groups because there is more than one structure that are
not identical that could be named as sec-pentyl or sec-hexyl.

H2 H2 H2 H2
C H CH3 C H C C CH
H 3C C H 3C C CH3 H3C C CH3
H2

sec -butyl NOT sec -pentyl

Tertiary (tert or t)
Starting with four carbon alkyl groups, there is an isomer which can have a connection to a tertiary carbon. These alkyl groups get
the prefix "t."

H 3C CH3 H2
H 3C C CH3
H 3C C H 2C C C C
H2
H 3C H 3C CH3 CH3
tert-butyl tert-pentyl tert-hexyl
or t-butyl or t-pentyl or t-hexyl

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Example:
The naming system described above is often used to describe halogens which contain only a few carbons. The halogen is shown as
bonded to the connection point of the alkyl group.
H 3C H 3C H2 H2 CH3
H 3C C Br C C H2C C Br
CH Br H 3C C Br
H 3C H 3C H2 H 3C CH3

isopropyl bromide t-butyl bromide n-butyl bromide tert-pentyl bromide

Classification of carbon atoms

Carbons have a special terminology to describe how many other carbons they are attached to. This allows for an easy description of
branching in alkanes. Also, we will find that the number of carbons attached to a given atom will have subtle effects on its
chemistry.
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.
The figure below use the group "R" to represent an alkyl group of unspecified length. R typically used to represent alkyl groups but
an also represent a part of a molecule which is either unspecified or not germane to the discussion.
R R R R
H C H H C R H C R R C R
H H R R

1° C 2° C 3° C 4° C

This terminology will be used repeatedly in organic chemistry to describe the number of carbons attached to a specific atom,
however, the atom will not always a carbon.

 Example 3.3.1

Please indicate the the number of 1o, 2o, 3o, and 4o carbons in the following molecule:
H CH3
H3C CH3
C C
H3C C CH3
H2

The molecule has six Primary carbons (1o).

The molecule has one Secondary carbon (2o).
The molecule has one Tertiary carbon (3o).
The molecule has one Quaternary carbon (4o)
3° C 2° C
H CH3
H 3C CH3
C C
H 3C C CH3
H2

1° C 4° C

Hydrogen atoms are also classified in this manner. A hydrogen atom attached to a primary carbon atom is called a primary
hydrogen ect.
R R R
H C H H C R H C R
H H R

1° H 2° H 3° H

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 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
It is not possible to have a quaternary hydrogen (4o).

 Example 3.3.2

Please indicate the the number of 1o, 2o, and 3o, hydrogens are in the following molecule:
H CH3
H 3C CH3
C C
H 3C C CH3
H2

The molecule has fifteen Primary (1o) hydrogens.

The molecule has two Secondary (2o) hydrogens.
The molecule has one Tertiary (3o) hydrogen.
3° H
H CH3
H 3C CH3
C C
H 3C C CH3
H2

1° H
2° H

Exercises

 Exercise 3.3.1

Determine whether the H’s indicated in the following structure are 1o, 2o, or 3o.
H H H H H H H H

H C C C C C C C C H

H H H H H H H H

Answer
H H H H H H H H
H C C C C C C C C H
H H H H H H H H

2o 2o 1o

 Exercise 3.3.2
Determine whether the H’s indicated in the following structure is 1o, 2o, or 3o.
CH3 CH3
H2
H3C C C CH
CH2 CH3
H3 C

Answer

3.3.4 https://chem.libretexts.org/@go/page/31400
 CH3 CH3
H2
1o H3C C C CH 3o
CH2 CH3 1o
H3 C

2o

 Exercise 3.3.3

Determine whether the carbons indicated in the structure below are 1o, 2o, 3o, or 4o.
CH3 CH3
H2
H3C C C CH
CH2 CH3
H3 C

Answer
4o
CH3 CH3
H2
H3C C C CH
CH2 CH3
3o
H3C

2o
1o

 Exercise 3.3.4

Determine whether the carbons indicated in the structure below are 1o, 2o, 3o, or 4o.

Answer
2o 2o
4o

1o

3o

 Exercise 3.3.5

Please indicate the total number of each type 1o, 2o, 3o, and 4o carbons in the following molecule.
H3C CH3
C CH3
H 2C C
H2
CH
H 3C CH3

Answer

3.3.5 https://chem.libretexts.org/@go/page/31400
 There are 5 primary (1o) C’s, 2 secondary (2o) C’s, 1 tertiary (3o) C and 1 quaternary (4o) C in the structure (seen color
coded below).
H3C CH3
C CH3
H 2C C
H2
CH
H 3C CH3

 Exercise 3.3.6

Please indicate the total number of each type 1o, 2o, 3o, and 4o carbons in the following molecule.

Answer
There are 8 primary (1o) C’s, 7 secondary (2o) C’s, 2 tertiary (3o) C’s and 2 quaternary (4o) C’s in the structure (seen color
coded below).

3.3: Alkyl Groups is shared under a CC BY-SA 4.0 license and was authored, remixed, and/or curated by Steven Farmer, Dietmar Kennepohl,
Zachary Sharrett, Krista Cunningham, Tim Soderberg, William Reusch, & William Reusch.

3.3.6 https://chem.libretexts.org/@go/page/31400
3.4: 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 3.4.1 : Simple Unbranched Alkanes
Molecular Structural Molecular Structural
Name Isomers Name Isomers
Formula Formula Formula Formula

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 Molecular Structural Molecular Structural
Name Isomers Name Isomers
Formula Formula Formula Formula

CH3(CH2)4C
methane CH4 CH4 1 hexane C6H14 5
H3

CH3(CH2)5C
ethane C2H6 CH3CH3 1 heptane C7H16 9
H3

CH3(CH2)6C
propane C3H8 CH3CH2CH3 1 octane C8H18 18
H3

CH3CH2CH2 CH3(CH2)7C
butane C4H10 2 nonane C9H20 35
CH3 H3

pentane C5H12 CH3(CH2)3CH3 3 decane C10H22 CH3(CH2)8CH3 75

 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):

A B C D 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 3.4.2 : Alkyl Groups Names
Group CH3– C2H5– CH3CH2CH2– (CH3)2CH– CH3CH2CH2CH
(CH
2– 3)2CHCH2C
– H3CH2CH(CH(CH
3)– 3)3C– R–

Name Methyl Ethyl Propyl Isopropyl Butyl Isobutyl sec-Butyl tert-Butyl Alkyl

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.

 Example 3.4.1 : Alkanes

A B C D E

The IUPAC names of the isomers of hexane are: A hexane B 2-methylpentane C 3-methylpentane D 2,2-dimethylbutane E 2,3-
dimethylbutane

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

 Example 3.4.2 : 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.

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.
CH4 CH3 R
methane methyl

CH3CH2CH3 CH3CH2CH2 R
propane propyl

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

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

3.4.3 https://chem.libretexts.org/@go/page/31401
Three Rules for 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
substituent 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
substituents and/or functional groups are written in alphabetical order.

 Example 3.4.3

What is the name of the follow molecule?

Solution
Rule #1: Choose the longest, most substituted carbon chain containing a functional group. This example 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 blue 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.

8 7 6 5 4 3 2 1

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 2,5-dimethyloctane

 Example 3.4.4

What is the name of the follow molecule?

Br Cl

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 blue and consists of seven carbons.
Br Cl

3.4.4 https://chem.libretexts.org/@go/page/31401
Rule #2: Carbons bonded to a functional group must have the lowest possible carbon number. If there are no functional groups,
then any substituent present must have the lowest possible number. In this example, numbering the chain from either 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.
Br Cl Br Cl

7 6 5 4 3 2 1 1 2 3 4 5 6 7

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.
Br Cl

1 2 3 4 5 6 7

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

 Example 3.4.5

What is the name of the follow molecule?

Br Cl

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 blue and consists of seven carbons.
Br Cl

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.
Br Cl

7 6 5 4 3 2 1

Br Cl

1 2 3 4 5 6 7

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

3.4.5 https://chem.libretexts.org/@go/page/31401
 Br Cl

7 6 5 4 3 2 1

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 Substitutents: 2-chloro 3-methyl 6-bromo
The name of this molecule is: 6-bromo-2-chloro-3-methylheptane

Exercises

 Exercise 3.4.1

Give the proper IUPAC names of the following compounds.

a)

b)

c)

Answer
a) Since this structure is an unbranched alkane (all single bonds) with a 5 carbon chain length, its name would be pentane.
b) This alkane has a 7 carbon longest continuous chain length that we number from right to left to get the first methyl
substituent we encounter to have the lowest possible number (3 versus being 4 if numbering from left to right). This causes
it to have 2 methyl substituents at positions 3 & 4 so we would name it indicating those numbers and the prefix dimethyl
which gives a proper IUPAC name of 3,4-dimethylheptane.
c) This alkane has a 5 carbon longest continuous chain length (which could be numbered from left to right or right to left
due to the symmetry at C-3). It has two methyl substituents off of C-3 so the proper IUPAC name is 3,3-dimethylpentane.
1 2
a) 4
3
5

7 5 3 1
b) 4
6 2

2 4
c) 3
5
1

 Exercise 3.4.2
Give the proper IUPAC names of the following compounds.

3.4.6 https://chem.libretexts.org/@go/page/31401
 a)

b)

c)

Answer
a) This alkane has a 9 carbon longest continuous chain length that we number from left to right (structure on left numbered
in blue) to make the ethyl substituent be number 4. For the structure on the right (numbered in red) going from right to left,
the methyl substituent is number 4. Since ethyl is higher in the alphabetical order, you want to make it have the lower
number so the structure on the left (blue numbering) takes priority and the name is 4-ethyl-6-methylnonane.
b) This alkane has a 6 carbon longest continuous chain length that we number from right to left to make the first methyl be
C-2 (versus the opposite direction which would make the first methyl C-3). Since there are 3 methyl substituents at
positions 2,3, & 4, this compound would have the name 2,3,4-trimethylhexane.
c) This 6 carbon alkane can be numbered along different chains (see below) as well as in the opposite directions. This
shows the two different chains that can be drawn (making the first substituent in that chain the lowest number). The
structure on the left (numbered in blue) is the correct choice since it causes more substituents to be on the longest
continuous chain (3 vs 2 in the structure on the right). This would make the IUPAC name of the structure 3-ethyl-2,4-
dimethylhexane. (Notice how ethyl takes priority over methyl and the di- is not considered for alphabetizing.)

2 8 vs 8 2
a) 1 1
4 6 9 6 4
3 5 7 9 7 5 3

b) 5 1
6 4
3
2

c) 4
3 6 vs 2 4
3 6
5
1 5
1 2

 Exercise 3.4.3

All of the following names represent a compound that has been named improperly. Draw out the structure from the name and
give the proper IUPAC name for the compounds.
a. 1,3-dimethylbutane
b. 4-ethylpentane
c. 2-ethyl-3-methylpentane

Answer

3.4.7 https://chem.libretexts.org/@go/page/31401
 a) The structure that can be drawn for the improper name is shown below on the left. When you renumber it properly
(structure on the right), the correct name should be 2-methylpentane.

1
a)
3 4 2
2 4 5 3 1

b) The structure that can be drawn for the improper name is shown below on the left. When you renumber it properly
(structure on the right), notice that the longest chain is 6 C’s and we start the numbering on the end to the right to make the
methyl substituent come off at C-3 (instead of beong at C-4 if we numbered it the opposite direction) the correct name
should be 3-methyl hexane.

b) 2 1
5
2 4 3
3 5 6 4
1

c) The structure that can be drawn for the improper name is shown below on the left. When you renumber it properly
(structure on the right), notice that the longest chain is 6 C’s and since this molecule is symmetrical (between carbon 3 &
4), you can start the numbers from either end. In this case, we have methyl substituents coming off of carbons 3 & 4 so the
proper name is 3,4-dimethyl hexane.

c) 1
2
3 3 5
2 4 4
5 6
1

 Exercise 3.4.4
All of the following names represent a compound that has been named improperly. Draw out the structure from the name and
give the proper IUPAC name for the compounds.
a. 2,2-diethylheptane
b. 2-propylpentane
c. 4,4-diethylbutane

Answer
a) The structure that can be drawn for the improper name is shown below on the left. When you renumber it properly
(structure on the right), notice that the longest chain is now 8 C’s and you have an ethyl substituent at C-3 and a methyl
substituent also at C-3 so the proper name is 3- ethyl-3-methyloctane.
1
a)
2
7
2 4 6 3 5
1 3 5 7 8
4 6

b) The structure that can be drawn for the improper name is shown below on the left. When you renumber it properly
(structure on the right), notice that the longest chain is now 7 C’s and since this molecule is symmetrical (at carbon 4), you
can start the numbers from either end. There is a methyl substituent at C-4 so the proper name is 4-methylheptane.
1
b)
2 3
6
2 4 7
3 5 4
1 5

c) The structure that can be drawn for the improper name is shown below on the left. When you renumber it properly
(structure on the right) going from right to left (to make the ethyl substituent have the lowest number possible), the correct
name is 3-ethylhexane

3.4.8 https://chem.libretexts.org/@go/page/31401
 c) 5 3 1
2 4
1 3 6 4 2

3.4: Naming Alkanes is shared under a CC BY-SA 4.0 license and was authored, remixed, and/or curated by Steven Farmer, Dietmar Kennepohl,
Zachary Sharrett, Krista Cunningham, Tim Soderberg, & Tim Soderberg.

3.4.9 https://chem.libretexts.org/@go/page/31401
3.5: 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 (also known as London Dispersion force)

Alkanes are not very reactive and have little biological activity; all alkanes are colorless and odorless non-polar compounds. The
relative weak London dispersion forces of alkanes result in gaseous substances for short carbon chains, volatile liquids with
densities around 0.7 g/mL for moderate carbon chains, and solids for long carbon chains. For molecules with the same functional
groups, there is a direct relationship between the size and shape of molecules and the strength of the intermolecular forces (IMFs)
causing the differences in the physical states.

Boiling Points
Table 3.5.1 describes some of the properties of some straight-chain alkanes. 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.
For 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.
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
17 36

have different melting and boiling points.

Table 3.5.1: Physical Properties of Some Alkanes
Physical State (at
Molecular Name Formula Melting Point (°C) Boiling Point (°C) Density (20°C)*
20°C)

methane CH4 –182 –164 0.668 g/L gas

ethane C2H6 –183 –89 1.265 g/L gas

propane C3H8 –190 –42 1.867 g/L gas

butane C4H10 –138 –1 2.493 g/L gas

pentane C5H12 –130 36 0.626 g/mL liquid

hexane C6H14 –95 69 0.659 g/mL liquid

octane C8H18 –57 125 0.703 g/mL liquid

decane C10H22 –30 174 0.730 g mL liquid

*Note the change in units going from gases (grams per liter) to liquids (grams per milliliter). Gas densities are at 1 atm pressure.

The boiling points for the "straight chain" isomers and isoalkanes isomers are shown to demonstrate that branching decreases the
surfaces area, weakens the IMFs, and lowers the boiling point.

3.5.1 https://chem.libretexts.org/@go/page/31402
  Example 3.5.1: Boiling Points of Alkanes

For example, the boiling points of the three isomers of C5 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 better able!

 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.

Solution
a. nonane, since it has more atoms it will have greater IMF
b. octane, since it is not branched, the molecules can pack closer together increasing IMF

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.

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  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. 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.

 Exercise 3.5.1

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.

Answer
Nonane will have a higher boiling point than octane, because it has a longer carbon chain than octane. 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

Reactions of Alkanes
Alkanes undergo very few reactions. There are two important reactions that are still possible, combustion and halogenation. The
halogenation reaction is very important in organic chemistry because it opens a gateway to further chemical reactions.

Combustion
Complete combustion (given sufficient oxygen) of any hydrocarbon produces carbon dioxide, water, and a significant amount of
heat. Due to the exothermic nature of these combustion reactions, alkanes are commonly used as a fuel source (for example:
propane for outdoor grills, butane for lighters). The hydrocarbons become harder to ignite as the molecules get bigger. This is
because the larger molecules don't vaporize as easily. If the liquid is not very volatile, only those molecules on the surface can react
with the oxygen. Larger molecules have greater Van der Waals attractions which makes it more difficult for them to break away
from their neighbors and become a gas. An example combustion reaction is shown for propane:

C H +O ⟶ 3 CO + 4 H O + 2044 kJ/mol
3 8 2 2 2

Halogenation
Halogenation is the replacement of one or more hydrogen atoms in an organic compound by a halogen (fluorine, chlorine, bromine
or iodine). Unlike the complex transformations of combustion, the halogenation of an alkane appears to be a simple substitution
reaction in which a C-H bond is broken and a new C-X bond is formed.
Since only two covalent bonds are broken (C-H & Cl-Cl) and two covalent bonds are formed (C-Cl & H-Cl), this reaction seems to
be an ideal case for mechanistic investigation and speculation. However, one complication is that all the hydrogen atoms of an
alkane may undergo substitution, resulting in a mixture of products, as shown in the following unbalanced equation. The relative
amounts of the various products depend on the proportion of the two reactants used. In the case of methane, a large excess of the
hydrocarbon favors formation of methyl chloride as the chief product; whereas, an excess of chlorine favors formation of
chloroform and carbon tetrachloride.

CH + Cl → CH Cl + CH Cl + CHCl + CCl + HCl

4 2 3 2 3 4

3.5.3 https://chem.libretexts.org/@go/page/31402
  Looking Closer: An Alkane Basis for Properties of Other Compounds
An understanding of the physical properties of alkanes is important since petroleum and natural gas and the many products
derived from them—gasoline, bottled gas, solvents, plastics, and more—are composed primarily of alkanes. This
understanding is also vital because it is the basis for describing the properties of other organic and biological compound
families. For example, large portions of the structures of lipids consist of nonpolar alkyl groups. Lipids include the dietary fats
and fat like compounds called phospholipids and sphingolipids that serve as structural components of living tissues. These
compounds have both polar and nonpolar groups, enabling them to bridge the gap between water-soluble and water-insoluble
phases. This characteristic is essential for the selective permeability of cell membranes.
O
H2 C O C CH2CH2CH2CH2CH2CH2CH2CH2CH2CH2CH2CH2CH2CH2CH3
O
(a)
HC O C CH2CH2CH2CH2CH2CH2CH2CH2CH2CH2CH2CH2CH2CH2CH3
O
H2 C O C CH2CH2CH2CH2CH2CH2CH2CH2CH2CH2CH2CH2CH2CH2CH3

(b) CH3CH2CH2CH2CH2CH2CH2CH2CH2CH2CH2CH2CH2CH2CH2CH3

Tripalmitin (a), a typical fat molecule, has long hydrocarbon chains typical of most lipids. Compare these chains to hexadecane
(b), an alkane with 16 carbon atoms.

3.5: Properties of Alkanes is shared under a CC BY-SA 4.0 license and was authored, remixed, and/or curated by Jim Clark, Steven Farmer,
Dietmar Kennepohl, Layne Morsch, Krista Cunningham, & Krista Cunningham.

3.5.4 https://chem.libretexts.org/@go/page/31402
3.6: 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 structural isomerism.
3. draw the conformers of ethane using 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)
dihedral angle
eclipsed conformation
Newman projection
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 clearly 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 of the
atoms 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 rotation of 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.
rotating bond

H H H HH H H
180° rotation 90° rotation
C C C C C C H
HH H HH H HH H
H

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.
H HH H
looking down the H H
C C carbon-carbon bond
HH H H
H H
“staggered” conformation
(Newman projection)

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.

3.6.1 https://chem.libretexts.org/@go/page/31403
 Figure 3.6.1: A 3D Model of Staggered Ethane.
The lowest energy conformation of ethane, shown in the figure above, is called the ‘staggered’ conformation. In the staggered
conformation, all of the C-H bonds on the front carbon are positioned at an angle of 60° relative to the C-H bonds on the back
carbon. This angle between a sigma bond on the front carbon compared to a sigma bond on the back carbon is called the dihedral
angle. In this conformation, the distance between the bonds (and the electrons in them) is maximized. Maximizing the distance
between the electrons decreases the electrostatic repulsion between the electrons and results in a more stable structure.
If we now rotate the front CH3 group 60° clockwise, the molecule is in the highest energy ‘eclipsed' conformation, and the
hydrogens on the front carbon are as close as possible to the hydrogens on the back carbon.
H H HH
C C H
H H
HH HH H
“eclipsed” conformation

This is the highest energy conformation because of unfavorable electrostatic repulsion between the electrons in the front and back
C-H bonds. The energy of the eclipsed conformation is approximately 3 kcal/mol (12 kJ/mol) higher than that of the staggered
conformation. Torsional strain (or eclipsing strain) is the name give to the energy difference caused by the increased electrostatic
repulsion of eclipsing bonds.
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. We will focus on the staggered and eclipsed conformers since they are, respectively, the lowest and highest energy
conformers.

Unhindered (Free) Rotations Do Not Exist in Ethane

The carbon-carbon bond is not completely free to rotate – the 3 kcal/mol torsional strain in ethane creates a barrier to rotation that
must be overcome for the bond to rotate from one staggered conformation to another. This rotational barrier is not large enough to
prevent rotation except at extremely cold temperatures. So at normal temperatures, the carbon-carbon bond is constantly rotating.
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 conformer. The potential energy associated with the various conformations of ethane varies with the
dihedral angle of the bonds, as shown in Figure 3.6.2.

Figure 3.6.2: The potential energy associated with the various conformations of ethane varies with the dihedral angle of the bonds.
Valleys in the graph represent the low energy staggered conformers, while peaks represent the higher energy eclipsed conformers.
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

3.6.2 https://chem.libretexts.org/@go/page/31403
 Figure 3.6.2: Animation of potential energy vs. dihedral angle in ethane

Exercises
1) What is the most stable rotational conformation of ethane and explain why it is preferred over the other conformation?

Solutions
1) Staggered, as there is less repulsion between the hydrogen atoms.
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.

3.6: Conformations of Ethane is shared under a CC BY-SA 4.0 license and was authored, remixed, and/or curated by Steven Farmer, Dietmar
Kennepohl, Krista Cunningham, William Reusch, & William Reusch.

3.6.3 https://chem.libretexts.org/@go/page/31403
3.7: 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 C2-C3 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 (strain)

In butane, there are three rotating carbon-carbon sigma 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.
H3C CH3 H3C CH3
C C H
H H
HH HH H
“eclipsed” (A)

Eclipsed interaction Energy (kcal/mol) Energy (kJ/mol)

H-H 1.0 4.0

H-CH3 1.4 6.0

CH3-CH3 2.6 11.0

The CH3-CH3 groups create the significantly larger eclipsed interaction of 11.0 kJ/mol. There are also two H-H eclipsed
interactions at 4.0 kJ/mol each to create a total of 2(4.0 kJ/mol) + 11.0 kJ/mol = 19.0 kJ/mol of strain. This is the highest energy
conformation for butane, due to torsional strain caused by the electrostatic repulsion of electrons in the eclipsed bonds, but also
because of another type of strain called ‘steric repulsion’, between the two rather bulky methyl groups. Steric strain comes about
when two large groups, such as two methyl groups, try to occupy the same space. What results is a repulsive non-covalent
interaction caused by their respective electron densities.
If we rotate the front, (blue) carbon by 60°clockwise, the butane molecule is now in a staggered conformation.
H 3C HCH CH3
3 H CH3
C C
HH H H
H H
gauche

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.

3.7.1 https://chem.libretexts.org/@go/page/31404
A further rotation of 60° gives us a second eclipsed conformation (B) in which both methyl groups are lined up with hydrogen
atoms.
H3 C H H3 C H
C C H
HH H H CH3
CH3 H
“eclipsed” (B)

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.
H3C HH CH3
H H
C C
HH H H
CH3 CH3
anti

The anti conformation is the lowest energy conformation for butane. The diagram below summarizes the relative energies for the
various eclipsed, staggered, and gauche conformations.
Figure 3.7.1 : A 3D Structure of the Anti Butane Conformer.

Figure 3.7.2 : Potential curve vs dihedral angle of the C2-C3 bond of butane.

Figure 3.7.2 : 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. Torsional/dihedral
angle is shown on x-axis. Conformation names (according to IUPAC): A: anti-periplanar, anti or trans B: synclinal or gauche C:
anticlinal or eclipsed D: syn-periplanar or cis. Source for conformation names & conformer classification: Pure & Appl. Chem.,
Vol. 68, No. 12, pp. 2193-2222, 1996. (Public Domain; Keministi).
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 the anti conformation at all carbon-carbon bonds. For example octane is commonly drawn as:

3.7.2 https://chem.libretexts.org/@go/page/31404
 H H H H H H
C C C CH3 =
H3 C C C C
H H H H H H

octane

Drawing Newman Projections

Newman projections are a valuable method for viewing the relative positions of groups within molecule. Being able to draw the
Newman projection for a given molecule is a valuable skill and will be used repeatedly throughout organic chemistry. Because
organic molecules often contain multiple carbon-carbon bonds it is important to precisely know which bond and which direction is
being sighted for the Newman projection. The details of the Newman projection change given the molecule but for typical alkanes
a full conformational analysis involves a full 360o rotation in 60o increments. This will produce three staggered conformers and
three eclipsed conformers. Typically, the staggered conformers are more stable and the eclipsed conformers are less stable. The
least stable conformer will have the largest groups eclipsed while the most stable conformer will have the largest groups anti (180o)
to each other.

Example
Draw the Newman projection of 2,3 dimethylbutane along the C2-C3 bond. Then determine the least stable conformation.
First draw the molecule and locate the indicated bond:
H3 C CH3
H C C H
H3 C CH3

Because the question asks for the least stable conformation, focus on the three possible eclipsed Newman projections. Draw out
three eclipsed Newman projections as a template. Because it is difficult to draw a true staggered Newman projection, it is common
to show the bonds slightly askew.

Place the substituents attached to the second carbon (C3) on the back bonds of all three Newman projections. In this example they
are 2 CH3s and an H. Place the substituents in the same position on all three Newman projections.
H3C H H3C CH3 H3C CH3
CH3 CH3 CH3
H3C CH3 H3C H H CH3
H H H

Then place the substituents attached to the first carbon (C2) on the front bonds of the Newman projection. In this example, the
substituents are also 2 CH3s and an H. Move the substituents through two 60o rotations to create the remaining two eclipsed
Newman projections. Leave the substituents on the back carbon in place. Attempting to rotate the front and back carbons
simultaneously is a common mistake and often leads to incorrect Newman projections.
H3C H H3C CH3 H3C CH3
CH3 CH3 CH3
H3C CH3 H3C H H CH3
H H H

Compare the Newman projections by looking the eclipsed interactions. Remember that the order of torsional strain interactions are
CH3-CH3 > CH3-H > H-H. The third structure has two CH3-CH3 torsional interactions which will make it the least stable
conformer of 2,3 dimethyl butane.
H3C CH3
CH3
H CH3
H

3.7.3 https://chem.libretexts.org/@go/page/31404
  Example 3.7.1
Draw Newman projections of the eclipsed and staggered conformations of propane, as if viewed down the C1-C2 bond.

Answer
H 3C H H 3C H
C C H
H H
HH HH H
highest energy
(eclipsed)

H 3C HH CH3
H H
C C
HH H H
H H
lowest energy
(staggered)

 Example 3.7.2

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

Answer

H H 3C H
H C CH3 H
C C
H CH2
H H H

Exercises
Questions
Q3.7.1
Draw the energy diagram for the rotation of the bond highlighted in pentane.

Solutions

S3.7.1

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3.7: Conformations of Other Alkanes is shared under a CC BY-SA 4.0 license and was authored, remixed, and/or curated by Jim Clark, Steven
Farmer, Dietmar Kennepohl, Krista Cunningham, Tim Soderberg, William Reusch, & William Reusch.

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3.8: 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 distillation procedure as it is performed in the
student laboratory.

Petroleum
The petroleum that is pumped out of the ground 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 abundance of the components vary depending on the source - 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 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) and becomes 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.

3.8.1 https://chem.libretexts.org/@go/page/31405
 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. (CC BY-NC-SA; anonymous)
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 are 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.

3.8.2 https://chem.libretexts.org/@go/page/31405
 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. (CC BY-NC-SA; anonymous)
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 Table 3.8.1, many compounds that are now available have octane ratings greater than 100, which means they are
better fuels than pure isooctane. In addition, anti-knock agents, also called octane enhancers, have been developed. One of the most
widely used for many years was tetraethyl lead [(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.
Table 3.8.1 : The Octane Ratings of Some Hydrocarbons and Common Additives
Condensed Structural Condensed Structural
Name Octane Rating Name Octane Rating
Formula Formula

CH3CH2CH2CH2CH2 skeletal structure of

n-heptane 0 o-xylene 107
CH2CH3 o-xylene.cdxml

CH3CH2CH2CH2CH2
n-hexane 25 ethanol CH3CH2OH 108
CH3

n-pentane CH3CH2CH2CH2CH3 62 t-butyl alcohol (CH3)3COH 113

CH3
(CH3)3CCH2CH(CH3
isooctane 100 p-xylene 116
)2 H3 C

benzene 106 methyl t-butyl ether H3COC(CH3)3 116

CH3

methanol CH3OH 107 toluene 118

3.8: Gasoline - A Deeper Look is shared under a CC BY-SA 4.0 license and was authored, remixed, and/or curated by Steven Farmer, Dietmar
Kennepohl, Krista Cunningham, & Krista Cunningham.

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3.S: Organic Compounds- Alkanes and Their Stereochemistry (Summary)
Concepts & Vocabulary

3.1: Functional Groups

Functional groups are atoms or small groups of atoms (two to four) that exhibit a characteristic reactivity.
Functional groups have characteristic names that often carry over into the naming of compounds.
The most common organic functional groups that will be encountered is this course are: alkanes, alkenes, alkynes, arenes, (alkyl
and aryl) halides, alcohols, ethers, aldehydes, ketones, esters, carboxylic acids, acid chlorides, amides, amines, nitriles, nitro
compounds, sulfides and sulfoxides.
3.2: Alkanes and Alkane Isomers
Hydrocarbons are a common class of organic molecules that contain only carbon and hydrogen atoms.
Alkanes are one type of hydrocarbon that contains only carbon-carbon and carbon hydrogen single bonds.
Straight chain and branched alkanes have the generic formula CnH2n+2, where n is equal to the number of carbons.
Cycloalkanes have the generic formula CnH2n.
Structural isomers are molecules with the same molecular formula, but different structures.
3.3: Alkyl Groups
Alkyl groups are small hydrocarbon chains attached to the parent alkane chain. The names of alkyl groups use the same prefixes
to indicate the number of carbons (meth-, eth-, etc.), but use "-yl" as the ending, instead of "-ane".
3.4: Naming Alkanes
The IUPAC System of nomenclature provides a set of rules for assigning every molecule a unique name.
3.5: Properties of Alkanes
The boiling point of an alkane depends upon molecular weight and number of branches in the chain. Boiling points tend to
increase with increasing molecular weight. Boiling points tend to decrease within a set of isomers as the number of branches
increases.
Alkanes and cycloalkanes are generally more soluble in organic solvents than in water.
3.6: Conformations of Ethane
Rotation about the carbon-carbon sigma bonds in ethane results in different rotational isomers (also known as conformational
isomers or conformers). Newman projections are a very common way of depicting conformers.
The two most common conformers of ethane are called staggered and eclipsed. The staggered conformer is lower in energy
(more stable) than the eclipsed conformer, because it has less torsional strain.
3.7: Conformations of Other Alkanes
Alkanes more complex than ethane, will have a greater variety of possible conformers. The anti and gauche conformers of
butane are specific types of staggered conformations.
3.8: Gasoline - A Deeper Look

Summary Problems

 Exercise 3.S. 1
Atorvastatin (Lipitor) is a synthetic pharmaceutical marketed by Pfizer for lowering blood cholesterol and is one of the top
selling drugs in the world. Circle and label all functional groups in Lipitor. (Be sure to label any amines or alcohols as primary,
secondary, or tertiary.)

3.S.1 https://chem.libretexts.org/@go/page/167947
 OH OH O
O
N OH
N
H

Answer
Tertiary
Amine
Secondary
Alcohol
Alkene

Carboxylic
Benzene Amide OH OH O Acid
O
N OH
N
H
Benzene

F
Benzene
Fluorine
Alkene

 Exercise 3.S. 2

Vincristine is a natural product that was originally isolated in 1958 and has been studied as an anticancer agent. Answer the
following questions related to this molecule. a) Circle and label all functional groups. (Be sure to label any amines or alcohols
as primary, secondary, or tertiary.) b) Clearly label one primary carbon, one secondary carbon, one tertiary carbon, and one
quaternary carbon.

OH
N
HN
O
N
O
O
O
N O
O HO O
O

Answer
tertiary
alkene
benzene tertiary alcohol primary carbon
(phenyl) amine OH
secondary carbon
secondary N
amine HN tertiary
O amine quaternary carbon
ester N
O alkene
O

ether O
N ester
benzene O
(phenyl) HO O
amide O
O

tertiary carbon ester

tertiary
alcohol

 Exercise 3.S. 3

Tamiflu (oseltamivir) is an anti-influenza medication that was discovered by Gilead Sciences and is marketed by the
pharmaceutical company Genetech. Circle and label all functional groups in Tamiflu. (Be sure to label any amines or alcohols
as primary, secondary, or tertiary.)

3.S.2 https://chem.libretexts.org/@go/page/167947
 O
O
O O

N
H
NH2

Answer
ether alkene

O ester
O
O O

N
H
NH2
amide
primary
amine

Notes: Alkanes are not functional groups, so there is no reason to circle groups like methyl or ethyl. (They are structural
fragments.) Also, this molecule does not contain an aromatic ring. This is a cyclohexene ring. An aromatic ring is benzene
and requires three double bonds in a six-membered ring.

 Exercise 3.S. 4

For the following structure, a) Draw a Newman projection looking down the C2-C3 bond. (C2 should be in front.) b) Rotate
the C2-C3 bond by 180 degrees (keep 3, 4, and 5 in the same orientation as the original structure). Draw the new skeletal
structure and the new Newman projection looking down the C2-C3 bond. c) Label the Newman projections from parts a and b
as staggered or eclipsed.
Br
4
3
5 2 1
OH

Answer
a)

H Br
HO H
CH3
staggered

b)
1
4 CH3
5 3
2 Br
H
OH Br H
HO
eclipsed

Skills to Master
Skill 3.1 Identify the following functional groups that are present in a given organic molecule: alkanes, alkenes, alkynes, arenes,
(alkyl and aryl) halides, alcohols, ethers, aldehydes, ketones, esters, carboxylic acids, acid chlorides, amides, amines, nitriles,
and nitro compounds.
Skill 3.2 Name and draw structures of straight chain alkanes up to ten carbons in length.
Skill 3.3 Name and draw structures for all the structural isomers of a given molecular formula.
Skill 3.4 Identify methyl, primary, secondary, tertiary, and quaternary carbons in organic structures.
Skill 3.5 Provide the IUPAC name of any given alkane or cycloalkane structure.

3.S.3 https://chem.libretexts.org/@go/page/167947
 Skill 3.6 Draw the structure of an alkane or cycloalkane given its IUPAC name.
Skill 3.7 Arrange a series of alkanes in order of increasing or decreasing boiling point.
Skill 3.8 Be able to draw Newman Projections of different conformers of alkanes.
Skill 3.9 be able evaluate a conformer in terms of torsional and steric strain.
Skill 3.10 Be able to identify the staggered, eclipsed, anti and gauche conformers of alkanes and to order them with respect to
relative energy.

Memorization Tasks (MT)

MT 3.1 Memorize the name and structure of each of the common functional groups listed in Skill 3.1.
MT 3.2 Memorize the names and be able to draw the first ten straight chain alkanes.
MT 3.3 Memorize the structures and common names of the alkyl substitutent groups - isopropyl, sec-butyl, isobutyl,, and tert-
butyl.

3.S: Organic Compounds- Alkanes and Their Stereochemistry (Summary) is shared under a CC BY-SA 4.0 license and was authored, remixed,
and/or curated by Kelly Matthews & Kevin M. Shea.

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 CHAPTER OVERVIEW
4: Organic Compounds - Cycloalkanes and their Stereochemistry
 Learning 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.

This chapter deals with the concept of stereochemistry and conformational analysis in cyclic compounds. The causes of various
ring strains and their effects on the overall energy level of a cycloalkane are discussed. We shall stress the stereochemistry of
alicyclic compounds.
4.1: Naming Cycloalkanes
4.2: Cis-Trans Isomerism in Cycloalkanes
4.3: Stability of Cycloalkanes - Ring Strain
4.4: Conformations of Cycloalkanes
4.5: Conformations of Cyclohexane
4.6: Axial and Equatorial Bonds in Cyclohexane
4.7: Conformations of Monosubstituted Cyclohexanes
4.8: Conformations of Disubstituted Cyclohexanes
4.9: Conformations of Polycyclic Molecules
4.S: Organic Compounds- Cycloalkanes and their Stereochemistry (Summary)

4: Organic Compounds - Cycloalkanes and their Stereochemistry is shared under a CC BY-SA 4.0 license and was authored, remixed, and/or
curated by Steven Farmer & Dietmar Kennepohl.

1
4.1: 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.

 Key Terms
Make certain that you can define, and use in context, the key terms below.
cycloalkane

 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.

Many organic compounds found in nature contain rings of carbon atoms. These compounds are known as cycloalkanes.
Cycloalkanes only contain carbon-hydrogen bonds and carbon-carbon single bonds. The simplest examples of this class consist of a
single, un-substituted carbon ring, and these form a homologous series similar to the unbranched alkanes.
Like alkanes, cycloalkane molecules are often drawn as skeletal structures in which each intersection between two lines is assumed
to have a carbon atom with its corresponding number of hydrogens. Cyclohexane, one of the most common cycloalkanes is shown
below as an example.
H2 H H
H H
C
H 2C CH2 H H
= =
H 2C CH2 H H
C
H2 H H
H H

Cyclic hydrocarbons have the prefix "cyclo-". The IUPAC names, molecular formulas, and skeleton structures of the cycloalkanes
with 3 to 10 carbons are given in Table 4.1.1. Note that the general formula for a cycloalkane composed of n carbons is CnH2n, and
not CnH2n+2 as for alkanes. Although a cycloalkane has two fewer hydrogens than the equivalent alkane, each carbon is bonded to
four other atoms so are still considered to be saturated with hydrogen.
Table 4.1.1 : Examples of Simple Cycloalkanes
Cycloalkane Molecular Formula Skeleton Structure

Cyclopropane C3H6

Cyclobutane C4H8

Cyclopentane C5H10

Cyclohexane C6H12

Cycloheptane C7H14

Cyclooctane C8H16

Cyclononane C9H18

Cyclodecane C10H20

4.1.1 https://chem.libretexts.org/@go/page/31408
IUPAC Rules for Nomenclature
The naming of substituted cycloalkanes follows the same basic steps used in naming alkanes.
1. Determine the parent chain.
2. Number the substituents of the ring beginning at one substituent so that the nearest substituent is numbered the lowest possible.
If there are multiple choices that are still the same, go to the next substituent and give it the lowest number possible.
3. Name the substituents and place them in alphabetical order.
More specific rules for naming substituted cycloalkanes with examples are given below.
1. Determine the cycloalkane to use as the parent. 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. Cycloalkanes substituents have an ending "-yl". If
there are two cycloalkanes in the molecule, use the cycloalkane with the higher number of carbons as the parent.

 Example 4.1.1

5
6

8 7 4 3
2
10 9

The longest straight chain contains 10 carbons, compared with cyclopropane, which only contains 3 carbons. The parent chain
in this molecule is decane and cyclopropane is a substituent. The name of this molecule is 3-cyclopropyl-6-methyldecane.

 Example 4.1.2

Name the cycloalkane structure.

Solution
There are two different cycloalkanes in this molecule. Because it contains more carbons, the cyclopentane ring will be named
as the parent chain. The smaller ring, cyclobutane, is named as a substituent on the parent chain. The name of this molecule is
cyclobutylcyclopentane.

2) When there is only one substituent on the ring, the ring carbon attached to the substituent is automatically carbon #1. Indicating
the number of the carbon with the substituent in the name is optional.

 Example 4.1.3
6
Cl 5
1
2
1
4 2
4 3
3

1-chlorocyclobutane or cholorocyclobutane 1-propylcyclohexane or propylcyclohexane

3) If there are multiple substituents on the ring, number the carbons of the cycloalkane so that the carbons with substituents 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.
4) When naming the cycloalkane, the substituents must be placed in alphabetical order. Remember the prefixes di-, tri-, etc. , are
not used for alphabetization.

4.1.2 https://chem.libretexts.org/@go/page/31408
 Example 4.1.4

1 5
2 4

3 1
3
2

In this example, the ethyl or the methyl subsistent could be attached to carbon one. The ethyl group attachment is assigned
carbon 1 because ethyl comes before methyl alphabetically. After assigning carbon 1 the cyclohexane ring can be numbered
going clockwise or counterclockwise. When looking at the numbers produced going clockwise produces lower first substituent
numbers (1,3) than when numbered counterclockwise (1,5). So the correct name is 1-ethyl-3-methylcyclohexane.

 Example 4.1.5

Name the following structure using IUPAC rules.

Br

CH3
CH3

Solution
Remember when dealing with cycloalkanes with more than two substituents, finding the lowest possible 2nd substituent
numbering takes precedence. Consider a numbering system with each substituent attachment point as being carbon one.
Compare them and whichever produces the lowest first point of difference will be correct.
The first structure would have 1,4 for the relationship between the first two groups. The next structure would have 1,3. The
final 2 structures both have 1,2 so those are preferable to the first two. Now we have to determine which is better between the
final 2 structures. The 3rd substituent on structure 3 would be at the 5 position leading to 1,2,5 while in the final structure the
3rd methyl group is on carbon 4 leading to 1,2,4. This follows the rules of giving the lowest numbers at the first point of
difference.

Br Br Br Br
1 1 5 4
2
2 4 3

3 1 2
3 3
4 CH3 CH3 2 CH3 1 CH3
CH3 CH3 CH3 CH3

The correct name for the molecule is 4-Bromo-1,2-dimethylcyclohexane.

 Example 4.1.6
Cl
1
5
Br
2

4 3
CH3

2-bromo-1-chloro-3-methylcyclopentane

4.1.3 https://chem.libretexts.org/@go/page/31408
 Notice that "b" of bromo alphabetically precedes the "m" of methyl. Also, notice that the chlorine attachment point is assigned
carbon 1 because it comes first alphabetically and the overall sum of numbers would be the same if the methyl attachment
carbon was assigned as 1 and the chlorine attachment as 3.

 Example 4.1.7
CH3
6
CH3
1
5
2
Br
4 3

(2-bromo-1,1-dimethylcyclohexane)
Although "di" alphabetically precedes "f", "di" is not used in determining the alphabetical order.

 Example 4.1.8
6 CH3
5 1 CH3
4
2
3 F

2-fluoro-1,1,-dimethylcyclohexane NOT 1,1-dimethyl-2-fluorocyclohexane

also
2-fluoro-1,1,-dimethylcyclohexane NOT 1-fluoro-2,2-dimethylcyclohexane (as that would give a larger number to the first
point of difference)
Although "di" alphabetically precedes "f", "di" is not used in determining the alphabetical order of the substituents. Notice that
the attachment point of the two methyl groups is assigned carbon 1 despite the fact that fluorine comes first alphabetically. This
is because this assignment allows for a lower overall numbering of substituents, so assigning alphabetical priority is not
necessary.

Polycyclic Compounds
Hydrocarbons having more than one ring are common, and are referred to as bicyclic (two rings), tricyclic (three rings) and in
general, polycyclic compounds. The molecular formulas of such compounds have H/C ratios that decrease with the number of
rings. In general, for a hydrocarbon composed of n carbon atoms associated with m rings the formula is: CnH . The 2 n+2 −2 m

structural relationship of rings in a polycyclic compound can vary. They may be separate and independent, or they may share one
or two common atoms. Some examples of these possible arrangements are shown in the following table.
Table 4.1.2 : Examples of Isomeric C 8
H
14
Bicycloalkanes
Isolated Rings Spiro Rings Fused Rings Bridged Rings

No common atoms One common atom One common bond Two common atoms

Polycyclic compounds, like cholesterol shown below, are biologically important and typically have common names accepted by
IUPAC. However, the common names do not generally follow the basic IUPAC nomenclature rules, and will not be covered here.

4.1.4 https://chem.libretexts.org/@go/page/31408
 H

H H
HO

Cholesterol (polycyclic)

 Exercise 4.1.1

Give the IUPAC names for the following cycloalkane structures.

CH3
a) b) c) CH3

CH3
CH2CH3

Br CH2CH3
H3 C
d) e) f) CH3

H3 C Cl
H3CH2C CH2CH3

Answer
a) 1,3-Dimethylcyclohexane
b) 2-Cyclopropylbutane
c) 1-Ethyl-3-methylcyclooctane
d) 1-Bromo-3-methylcyclobutane
e) 1,2,4-Triethylcycloheptane
f) 1-Chloro-2,4-dimethylcyclopentane

 Exercise 4.1.2

Draw the structures for the IUPAC names below.

a. 2,3-dicyclopropylpentane
b. 1,2,3-triethylcyclopentane
c. 3-cyclobutyl-2-methylhexane
d. 2-bromo-1-chloro-4-methylcyclohexane
e. 1-bromo-5-propylcyclododecane

Answer

4.1.5 https://chem.libretexts.org/@go/page/31408
 CH3
CH2CH3
a) b) c)
H3CH2C
CH2CH3

CH2CH3

2,3-dicyclopropylpentane 1,2,3-triethylcyclopentane 3-cyclobutyl-2-methylhexane

Br

d) e) Br
Cl

CH3

1-bromo-5-propylcyclodecane
2-bromo-1-chloro-4-methylcyclohexane

4.1: Naming Cycloalkanes is shared under a CC BY-SA 4.0 license and was authored, remixed, and/or curated by Jim Clark, Steven Farmer,
Dietmar Kennepohl, Zachary Sharrett, Layne Morsch, Krista Cunningham, Tim Soderberg, Pwint Zin, Kelly Matthews, & Kelly Matthews.

4.1.6 https://chem.libretexts.org/@go/page/31408
4.2: Cis-Trans Isomerism in Cycloalkanes
 Objectives

After completing this section, you should be able to

1. draw structural formulas that distinguish between cis and trans disubstituted cycloalkanes.
2. 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.
constitutional isomer
stereoisomer
cis-trans isomers

Previously, constitutional isomers have been defined as molecules that have the same molecular formula, but different atom
connectivity. In this section, a new class of isomers, stereoisomers, will be introduced. Stereoisomers are molecules that have the
same molecular formula, the same atom connectivity, but they differ in the relative spatial orientation of the atoms.
Cycloalkanes are similar to open-chain alkanes in many respects. They both tend to be nonpolar and relatively inert. One important
difference, is that cycloalkanes have much less freedom of movement than open-chain alkanes. As discussed in Sections 3.6 and
3.7, open-chain alkanes are capable of rotation around their carbon-carbon sigma bonds. The ringed structures of cycloalkanes
prevent such free rotation, causing them to be more rigid and somewhat planar.
Di-substituted cycloalkanes are one class of molecules that exhibit stereoisomerism. 1,2-dibromocyclopentane can exist as two
different stereoisomers: cis-1,2-dibromocyclopentane and trans-1,2-dibromocyclopentane. The cis-1,2-dibromocyclopentane and
trans-1,2-dibromocyclopentane stereoisomers of 1,2-dibromocyclopentane are shown below. Both molecules have the same
molecular formula and the same atom connectivity. They differ only in the relative spatial orientation of the two bromines on the
ring. In cis-1,2-dibromocyclopentane, both bromine atoms are on the same "face" of the cyclopentane ring, while in trans-1,2-
dibromocyclopentane, the two bromines are on opposite faces of the ring. Stereoisomers require an additional nomenclature prefix
be added to the IUPAC name in order to indicate their spatial orientation. Di-substituted cycloalkane stereoisomers are designated
by the nomenclature prefixes cis (Latin, meaning on this side) and trans (Latin, meaning across).

H
Br Br Br
= cis -1,2-dibromocyclopentane
H
Br H
H

H
Br H Br
= trans -1,2-dibromocyclopentane
H
H Br
Br

The 3D Structure of cis-1,2-dibromocyclopentane

The 3D Structure of trans-1,2-dibromocyclopentane

Representing 3D Structures
By convention, chemists use heavy, wedge-shaped bonds to indicate a substituent located above the plane of the ring (coming out
of the page), a dashed line for bonds to atoms or groups located below the ring (going back into the page), and solid lines for bonds
in the plane of the page.

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 CH3
CH3

H 3C
CH3
Br

cis -1,3-dimethylcyclobutane trans -5-bromo-1,4,6-trimethyl-1,3-cycloheptadiene

CH3
CH3

Cl Cl

trans -2,4-dichloro-1,1-dimethylcyclohexane cis -3,5-divinylcyclopentene

In general, if any two sp3 carbons in a ring have two different substituent groups (not counting other ring atoms) cis/trans
stereoisomerism is possible. However, the cis/trans designations are not used if both groups are on the same carbon. For example,
the chlorine and the methyl group are on the same carbon in 1-chloro-1-methylcyclohexane and the trans prefix should not be used.
Cl
CH3

1-chloro-1-methylcyclohexane

If more than two ring carbons have substituents, the stereochemical notation distinguishing the various isomers becomes more
complex and the prefixes cis and trans cannot be used to formally name the molecule. However, the relationship of any two
substituents can be informally described using cis or trans. For example, in the tri-substituted cyclohexane below, the methyl group
is cis to the ethyl group, and also trans to the chlorine. However, the entire molecule cannot be designated as either a cis or trans
isomer. Later sections will describe how to name these more complex molecules (5.5: Sequence Rules for Specifying
Configuration)
CH3

Cl CH2CH3

 Example 4.2.1

Name the following cycloalkanes:

a) Br b)
H3C H
H
Br H CH3
H

Solution
These two example represent the two main ways of showing spatial orientation in cycloalkanes.
a) In example "a" the cycloalkane is shown as being flat and in the plane of the page. The positioning of the substituents is
shown by using dash-wedge bonds. Cis/trans positioning can be determined by looking at the type of bonds attached to the
substituents. If the substituents are both on the same side of the ring (Cis) they would both have either dash bonds or wedge
bonds. If the the substituents are on opposite side of the ring (Trans) one substituent would have a dash bond and the other a
wedge bond. Because both bromo substituents have a wedge bond they are one the same side of the ring and are cis. The name
of this molecule is cis-1,4-Dibromocyclohexane.
b) Example "b" shows the cycloalkane ring roughly perpendicular to the plane of the page. When this is done, the upper and
lower face of the ring is defined and each carbon in the ring will have a bond one the upper face and a bond on the lower face.
Cis substituents will either both be on the upper face or the lower face. Trans substituents will have one on the upper face and

4.2.2 https://chem.libretexts.org/@go/page/31409
 one one the lower face. In example "b", one of the methyl substituents is on the upper face of the ring and one is on the lower
face which makes them trans to each other. The name of this molecule is trans-1,2-Dimethylcyclopropane.

Exercises

 Exercise 4.2.1

Draw the following molecules:

1. trans-1,3-dimethylcyclohexane
2. trans-1,2-dibromocyclopentane
3. cis-1,3-dichlorocyclobutane

Answer

2) Cis/Trans nomenclature can be used to describe the relative positioning of substituents on molecules with more complex ring
structures. The molecule below is tesosterone, the primary male sex hormone. Is the OH and the adjacent methyl group cis or trans
to each other? What can you deduce about the relative positions of the indicated hydrogens?

3) Name the following compounds:

4.2.3 https://chem.libretexts.org/@go/page/31409
Solutions
2) Both the OH and the methyl group have wedge bonds. This implies that they are both on the same side of the testosterone ring
making them cis. Two of the hydrogens have wedge bonds while one has a wedge. This means two of the hydrogens are on one
side of the testosterone ring while one is on the other side.
3)
Cis-1-Bromo-3-Chlorocyclobutane
Trans-1,4-Dimethylcyclooctane
Trans-1-Bromo-3-ethylcyclopentane

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

4.2: Cis-Trans Isomerism in Cycloalkanes is shared under a CC BY-SA 4.0 license and was authored, remixed, and/or curated by Steven Farmer,
Dietmar Kennepohl, Krista Cunningham, Kelly Matthews, & Kelly Matthews.

4.2.4 https://chem.libretexts.org/@go/page/31409
4.3: 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 provides information about the amount of strain present in a
cycloalkane ring.
3. determine the relative stability of cyclic compounds, 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
steric strain
torsional strain
ring strain
heat of combustion

Heat of Combustion as a Measure of Bond Strength

The combustion of carbon compounds, especially hydrocarbons, has been the most important source of heat energy for human
civilizations throughout recorded history. The practical importance of this reaction cannot be denied, but the massive and
uncontrolled chemical changes that take place in combustion make it difficult to deduce mechanistic paths. Using the combustion
of propane as an example, we see from the following equation that every covalent bond in the reactants has been broken and an
entirely new set of covalent bonds have formed in the products. No other common reaction involves such a profound and pervasive
change, and the mechanism of combustion is so complex that chemists are just beginning to explore and understand some of its
elementary features.

CH CH CH +5 O ⟶ 3 CO + 4 H O + heat
3 2 3 2 2 2

Since all the covalent bonds in the reactant molecules are broken, the quantity of heat evolved in this reaction, and any other
combustion reaction, is related to the strength of these bonds (and, of course, the strength of the bonds formed in the products).
Precise heat of combustion measurements can provide useful information about the structure of molecules and their relative
stability.
For example, heat of combustion is useful in determining the relative stability of isomers. Pentane has a heat of combustion of -782
kcal/mol, while that of its isomer, 2,2-dimethylpropane (neopentane), is –777 kcal/mol. These values indicate that 2,3-
dimethylpentane is 5 kcal/mol more stable than pentane, since it has a lower heat of combustion.

Ring Strain
Table 4.3.1 lists the heat of combustion data for some simple cycloalkanes. These cycloalkanes do not have the same molecular
formula, so the heat of combustion per each CH2 unit present in each molecule is calculated (the fourth column) to provide a useful
comparison. From the data, cyclopropane and cyclobutane have significantly higher heats of combustion per CH2, while
cyclohexane has the lowest heat of combustion. This indicates that cyclohexane is more stable than cyclopropane and cyclobutane,
and in fact, that cyclohexane has a same relative stability as long chain alkanes that are not cyclic. This difference in stability is
seen in nature where six membered rings are by far the most common. What causes the difference in stability or the strain in small
cycloalkanes?
Table 4.3.1 : Heats of combustion of select hydrocarbons
Cycloalkane CH2 Units ΔH25º ΔH25º Ring Strain
(CH2)n n kcal/mol per CH2 Unit kcal/mol

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 Cycloalkane CH2 Units ΔH25º ΔH25º Ring Strain
(CH2)n n kcal/mol per CH2 Unit kcal/mol

Cyclopropane n=3 468.7 156.2 27.6

Cyclobutane n=4 614.3 153.6 26.4

Cyclopentane n=5 741.5 148.3 6.5

Cyclohexane n=6 882.1 147.0 0.0

Cycloheptane n=7 1035.4 147.9 6.3

Cyclooctane n=8 1186.0 148.2 9.6

Cyclononane n=9 1335.0 148.3 11.7

Cyclodecane n = 10 1481 148.1 11.0

CH3(CH2)mCH3 m = large — 147.0 0.0

The Baeyer Theory on the Strain in Cycloalkane Rings

In 1890, the famous German organic chemist, A. Baeyer, suggested that cyclopropane and cyclobutane are less stable than
cyclohexane, because the the smaller rings are more "strained". There are many different types of strain that contribute to the
overall ring strain in cycloalkanes, including angle strain, torsional strain, and steric strain. Torsional strain and steric strain were
previously defined in the discussion of conformations of butane. Angle Strain occurs when the sp3 hybridized carbons in
cycloalkanes do not have the expected ideal bond angle of 109.5o, causing an increase in the potential energy. An example of angle
strain can be seen in the diagram of cyclopropane below in which the bond angle is 60o between the carbons. The compressed bond
angles causes poor overlap of the hybrid orbitals forming the carbon-carbon sigma bonds which in turn creates destabilization.

H2
C

109.5° 60°
H 2C CH2

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 be less stable than molecules such as cyclohexane and
cyclopentane, which have a much lower ring strain because the bond angle between the carbons is much closer to 109.5o. Changes
in chemical reactivity as a consequence of angle strain are dramatic in the case of cyclopropane, and are also evident for
cyclobutane.
In addition to angle strain, there is also steric (transannular) strain and torsional strain in many cycloalkanes. Transannular strain
exists when there is steric repulsion between atoms.
H3 C
CH3
steric repulsion
CH3

transannular strain

Because cycloalkane lack the ability to freely rotate, torsional (eclipsing) strain exists when a cycloalkane is unable to adopt a
staggered conformation around a C-C bond. Torsional strain is especially prevalent in small cycloalkanes, such as cyclopropane,
whose structures are nearly planar.

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 The Eclipsed C-H Bonds in Cyclopropane
Larger rings like cyclohexane, deal with torsional strain by forming conformers in which the rings are not planar. 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, which decreases the angle and torsional strain
in the ring. The non-planar structures of cyclohexane are very stable compared to cyclopropane and cyclobutane, and will be
discussed in more detail in the next section.
H
HH
H
H
H H
H
H
HH H
cyclohexane cyclohexane chair conformer
(more stable)

The Types of Strain Which Contribute to Ring Strain in Cycloalkanes

Angle Strain The strain caused by the increase or reduction of bond angles

Torsional Strain The strain caused by eclipsing bonds on adjacent atoms

The strain caused by the repulsive interactions of atoms trying to

Steric Strain
occupy the same space

 Exercise 4.3.1

trans-1,2-Dimethylcyclobutane is more stable than cis-1,2-dimethylcyclobutane. Explain this observation.

Answer
The trans form does not have eclipsing methyl groups, therefore lowering the energy within the molecule. It does however
have hydrogen-methyl eclipsing interactions which are not as high in energy as methyl-methyl interactions.

 Exercise 4.3.2

Cyclobutane has more torsional stain than cyclopropane. Explain this observation.

Answer
Cyclobutane has 4 CH2 groups while cyclopropane only has 3. More CH2 groups means cyclobutane has more eclipsing H-
H interactions and therefore has more torsional strain.

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.

4.3.3 https://chem.libretexts.org/@go/page/31410
4.3: Stability of Cycloalkanes - Ring Strain is shared under a CC BY-SA 4.0 license and was authored, remixed, and/or curated by Steven Farmer,
Dietmar Kennepohl, Krista Cunningham, Tim Soderberg, William Reusch, Kelly Matthews, & Kelly Matthews.

4.3.4 https://chem.libretexts.org/@go/page/31410
4.4: 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 use this to account for the high reactivity of this compound.
3. analyze 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 cyclobutane cyclopentane cyclohexane cycloheptane cyclooctane

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 40 kJ/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 360º, going through many
different conformations. That complete rotation isn't possible in a cyclic system, because the parts that would be trying to twist
away from each other would still be connected together. Thus 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. This lack of flexibility does not allow cyclopropane to form more stable
conformers which are non-planar.

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 H H
H
H H
cyclopropane H

The main source of ring strain in cyclopropane is angle strain. All of the carbon atoms in cyclopropane are tetrahedral and would
prefer to have a bond angle of 109.5o The angles in an equilateral triangle are actually 60o, about half as large as the optimum
angle. The large deviation from the optimal bond angle means that the C-C sigma bonds forming the cyclopropane ring are bent.
Maximum bonding occurs when the overlapping orbitals are pointing directly toward each other. The severely strained bond angles
in cyclopropane means that the orbitals forming the C-C bonds overlap at a slight angle making them weaker. This strain is
partially overcome by using so-called “banana bonds”, where the overlap between orbitals is no longer directly in a line between
the two nuclei, as shown here in three representations of the bonding in cyclopropane:
HH
C

H C C H
H H

The constrained nature of cyclopropane causes neighboring C-H bonds to all be held in eclipsed conformations. Cyclopropane is
always at maximum torsional strain. This strain can be illustrated in a Newman projections of cyclopropane as shown from the
side.
HH

HH

Newman Projection of cyclopropane

Cyclopropane isn't large enough to introduce any steric strain. Steric strain does not become a factor until we reach six membered
rings. Before that point, rings are not flexible enough to allow for two ring substituents to interact with each other.
The combination of torsional and angle strain creates a large amount of ring strain in cyclopropane which weakens the C-C ring
bonds (255 kJ/mol) when compared to C-C bonds in open-chain propane (370 kJ/mol).

Cyclobutane
Cyclobutane is a four membered ring. The larger number of ring hydrogens would cause a substantial amount of torsional strain if
cyclobutane were planar.

cyclobutane

In three dimensions, cyclobutane is flexible enough to buckle into a "puckered" shape which causes the C-H ring hydrogens to
slightly deviate away from being completely eclipsed. This conformation relives some of the torsional strain but increases the angle
strain because the ring bond angles decreases to 88o.
In a line drawing, this butterfly shape is usually shown from the side, with the near edges drawn using darker lines.
H H
H
H H
H
H
H

The deviation of cyclobutane's ring C-H bonds away from being fully eclipsed can clearly be seen when viewing a Newman
projections signed down one of the C-C bond.
HH

HH

Newman projection of cyclobutane

With bond angles of 88o rather than 109.5o degrees, cyclobutane has significant amounts of angle strain, but less than in
cyclopropane.

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 Although torsional strain is still present, the neighboring C-H bonds are not exactly eclipsed in the cyclobutane's puckered
conformation.
Steric strain is very low. Cyclobutane is still not large enough that substituents can reach around to cause crowding.
Overall the ring strain in cyclobutane (110 kJ/mol) is slightly less than cyclopropane (115 kJ/mol).

Cyclopentane
Cyclopentanes are even more stable than cyclobutanes, and they are the second-most common cycloalkane ring in nature, after
cyclohexanes. Planar cyclopentane has virtually no angle strain but an immense amount of torsional strain. To reduce torsional
strain, cyclopentane addops a non-planar conformation even though it slightly increases angle strain.

cyclopentane

The lowest energy conformation of cyclopentane is known as the ‘envelope’, with four of the ring atoms in the same plane and one
out of plane (notice that this shape resembles an envelope with the flap open). The out-of-plane carbon is said to be in the endo
position (‘endo’ means ‘inside’). The envelope removes torsional strain along the sides and flap of the envelope. However, the
neighboring carbons are eclipsed along the "bottom" of the envelope, away from the flap.
H
HH H
H
H
H
H HH

3D structure of cyclopentane (notice that the far top right carbon is the endo position).
At room temperature, cyclopentane undergoes a rapid bond rotation process in which each of the five carbons takes turns being in
the endo position.

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. The envelope removes torsional strain along the sides and flap of the envelope by allowing the bonds to be in an
almost completely staggered position. However, the neighboring bonds are eclipsed along the "bottom" of the envelope, away from
the flap. Viewing a Newman projections of cyclopentane signed down one of the C-C bond show the staggered C-H bonds.

HH

HH

Newman projection of cyclopentane

The angle strain in the envelope conformation of cyclopentane is low. The ideal angle in a regular pentagon is about 107o, very
close to the preferred 109.5o tetrahedral bond angle.
There is some torsional strain in cyclopentane. The envelope conformation reduces torsional strain by placing some bonds in
nearly staggered positions. However, other bonds are still almost fully eclipsed.
Cyclopentane is not large enough to allow for steric strain to be created.
Overall, cyclopentane has very little ring strain (26 kJ/mol) when compared to cyclopropane and cyclobutane.

C3-C5 Cycloalkanes in Nature

If one of the carbon-carbon bonds is broken in cyclopropane or cyclobutane, the ring will ‘spring’ open, releasing energy as the
bonds reassume their preferred tetrahedral geometry. The effectiveness of two antibiotic drugs, fosfomycin and penicillin, is due in
large part to the high reactivity of the three- and four-membered rings in their structures.

4.4.3 https://chem.libretexts.org/@go/page/31411
 H
O N S
H H O CH3
O N CH3
H3C O P O
O
O O
O
fosfomycin penicillin G

One of the most important five-membered rings in nature is a sugar called ribose – DNA and RNA are both constructed upon
‘backbones’ derived from ribose. Pictured below is one thymidine (T) deoxy-nucleotide from a stretch of DNA. Since the ribose
has lost one of the OH groups (at carbon 2 of the ribose ring), this is part of a deoxyribonucleic acid (DNA). If the OH at carbon 2
of the ribose ring was present, this would be part of a ribonucleic acid (RNA).
DNA

O H
O
HO N
O P O O
O OH O
O N
CH3
HO OH O
(no OH group
here in DNA)
ribose DNA

The lowest-energy conformations for ribose are envelope forms in which either C3 or C2 are endo, on the same side as the C5
substituent.
OH

HO
O OH

OH

Exercises
1) If cyclobutane were to be planar, how many H-H eclipsing interactions would there be? Assuming 4 kJ/mol per H-H eclipsing
interaction what would the strain be on this “planar” molecule?
2) In the two conformations of trans-1,2-Dimethylcyclopentane one is more stable than the other. Explain why this is.

3) In methylcyclopentane, which carbon would most likely be in the endo position?

Solutions
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).
2) The first conformation is more stable. Even though the methyl groups are trans in both models, they are anti to one another in
the first structure (which is lower energy) while they are gauche in the second structure increasing strain within the molecule.
3) The ring carbon attached to the methyl group would most likely be the endo carbon. The large methyl group would create the
most torsional strain if eclipsed. Being in the endo position would place the bonds is a more staggered position which would reduce
strain.
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

4.4.4 https://chem.libretexts.org/@go/page/31411
In the two conformations of trans-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 trans in both models, in the second structure they are
eclipsing one another, therefore increasing the strain within the molecule compared to the first structure where the larger methyl
groups are anti to one another.

4.4: Conformations of Cycloalkanes is shared under a CC BY-SA 4.0 license and was authored, remixed, and/or curated by Chris Schaller, Steven
Farmer, Dietmar Kennepohl, Layne Morsch, Krista Cunningham, William Reusch, & William Reusch.

4.4.5 https://chem.libretexts.org/@go/page/31411
4.5: 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 structure of a cyclohexane ring in the chair conformation.

 Key Terms
Make certain that you can define, and use in context, the key terms below.
chair conformation
twist-boat conformation

We will find that cyclohexanes tend to have the least angle strain and consequently are the most common cycloalkanes found in
nature. A wide variety of compounds including, hormones, pharmaceuticals, and flavoring agents have substituted cyclohexane
rings.
OH

H H
O

testosterone, which contains three cyclohexane rings and one cyclopentane ring
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).
Cyclohexane has the possibility of forming multiple conformations each of which have structural differences which lead to
different amounts of ring strain.
H H
H H H H H H
H H H H
H H H H H H H
H H H H H
H H H H H H
H H H H H
H
H
H HH H H H
H H

boat conformation twist boat conformation chair conformation

planar structure
slight angle strain slight angle strain no angle strain
severe angle strain (120°)
eclipsing strain at two bonds small eclipsing strain no eclipsing strain
severe eclipsing strain (all bonds)
steric crowding of two hydrogens small steric strain small steric strain
small steric strain

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-hydrogen bond in such a structure would be eclipsed. The resulting angle and eclipsing
strains would severely destabilize this structure. The ring strain of planar cyclohexane is in excess of 84 kJ/mol so it rarely
discussed other than in theory.

4.5.1 https://chem.libretexts.org/@go/page/31412
 Cyclohexane in the strained planar configuration showing how the hydrogens become eclipsed.
Chair Conformation of Cyclohexane
The flexibility of cyclohexane allows for a conformation which is almost free of ring strain. If two carbon atoms on opposite sides
of the six-membered ring are bent out of the plane of the ring, a shape is formed that resembles a reclining beach chair. This chair
conformation is the lowest energy conformation for cyclohexane with an overall ring strain of 0 kJ/mol. In this conformation, the
carbon-carbon ring bonds are able to assume bonding angles of ~111o which is very near the optimal tetrahedral 109.5o so angle
strain has been eliminated.
H H
H H
H C C H
C =
H C
C C H
H H
H H

Also, the C-H ring bonds are staggered so torsional strain has also been eliminated. This is clearly seen when looking at a Newman
projection of chair cyclohexane sighted down the two central C-C bonds.
H H2 H
H C H
H C H
H H2 H

Newman projection of cyclohexane

How to Draw the Chair Conformation

To draw a chair: 1) Draw two 2) Draw another pair of 3) Connect with

slightly offset parallel lines from the a third set of
parallel lines. ends of the first pair. parallel lines.

To draw its ring-flip conformer, just start the first pair of lines at the opposite angle.

Boat Conformation of Cyclohexane

The Boat Conformation of cyclohexane is created when two carbon atoms on opposite sides of the six-membered ring are both
lifted up out of the plane of the ring creating a shape which slightly resembles a boat. The boat conformation is less stable than the
chair form for two major reasons. The boat conformation has unfavorable steric interactions between a pair of 1,4 hydrogens (the
so-called "flagpole" hydrogens) that are forced to be very close together (1.83Å). This steric hindrance creates a repulsion energy
of about 12 kJ/mol. An additional cause of the higher energy of the boat conformation is that adjacent hydrogen atoms on the
'bottom of the boat' are forced into eclipsed positions. For these reasons, the boat conformation about 30 kJ/mol less stable than the
chair conformation.
H H
H H

A boat structure of cyclohexane (the interfering "flagpole" hydrogens are shown in red)

4.5.2 https://chem.libretexts.org/@go/page/31412
Twist-Boat Conformation of Cyclohexane
The boat form is quite flexible and by twisting it at the bottom created the twist-boat conformer. This conformation reduces the
strain which characterized the boat conformer. The flagpole hydrogens move farther apart (the carbons they are attached to are
shifted in opposite directions, one forward and one back) and the eight hydrogens along the sides become largely but not
completely staggered. Though more stable than the boat conformation, the twist-boat (sometimes skew-boat) conformation is
roughly 23 kJ/mol less stable than the chair conformation.
H H
H
H

A twist-boat structure of cyclohexane

Half Chair Conformation of Cyclohexane
Cyclohexane can obtain a partially plane conformation called "half chair" but with only with excessive amounts of ring strain. The
half chair conformation is formed by taking planar cyclohexane and lifting one carbon out of the plane of the ring. The half chair
conformation has much of the same strain effects predicted by the fully planar cyclohexane. In the planar portion of half chair
cyclohexane the C-C bond angles are forced to 120o which creates significant amounts of angle strain. Also, the corresponding C-H
bonds are fully eclipsed which create torsional strain. The out-of-plane carbon allows for some of the ring's bond angles to reach
109.5o and for some of C-H bonds to not be fully eclipsed. Overall, the half chair conformation is roughly 45 kJ/mol less stable
than the chair conformation.

Conformation Changes in Cyclohexane - "Ring Flips"

Cyclohexane is rapidly rotating between the two most stable conformations known as the chair conformations in what is called the
"ring flip" shown below. The importance of the ring flip will be discussed in the next section.

"Ring flip" describes the rapid equilibrium of cyclohexane rings between the two chair conformations
rotate this carbon down

rotate this carbon up

axial
H H UP H H
H H H H
H H H H equatorial
H H H H UP
H H H H
equatorial axial
H H DOWN H H
DOWN

It is important to note that one chair does not immediately become the other chair, rather the ring must travel through the higher
energy conformations as transitions. At room temperature the energy barrier created by the half chair conformation is easily
overcome allowing for equilibration between the two chair conformation on the order of 80,000 times per second. Although
cyclohexane is continually converting between these different conformations, the stability of the chair conformation causes it to
comprises more than 99.9% of the equilibrium mixture at room temperature.

4.5.3 https://chem.libretexts.org/@go/page/31412
 1" id="MathJax-Element-12-Frame" role="presentation" style="position:relative;" tabindex="0">Image of energy diagram of
cyclohexane conformations
1" role="presentation" style="position:relative;" tabindex="0">

Exercises
1) Consider the conformations of cyclohexane: half chair, chair, boat, twist boat. Order them in increasing ring strain in the
molecule.

Solutions
1) Chair < Twist Boat < Boat < half chair (most ring strain)
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)

4.5: Conformations of Cyclohexane is shared under a CC BY-SA 4.0 license and was authored, remixed, and/or curated by Steven Farmer,
Dietmar Kennepohl, Layne Morsch, Krista Cunningham, William Reusch, Robert Bruner, & Robert Bruner.

4.5.4 https://chem.libretexts.org/@go/page/31412
4.6: Axial and Equatorial Bonds in Cyclohexane
 Objectives

After completing this section, you should be able to

1. Draw the chair conformation 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

Axial and Equatorial Positions in Cyclohexane

Careful examination of the chair conformation of cyclohexane, shows 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.
H Hax
H H
H Heq
H H
H H
H H

In the figure above, the equatorial hydrogens are colored blue, and the axial hydrogens are black. Since there are two equivalent
chair conformations of cyclohexane in rapid equilibrium, all twelve hydrogens have 50% equatorial and 50% axial character.

How To Draw Axial and Equatorial Bonds

corner pointing
down, so axial
bond goes down

corner pointing
up, so axial
bond goes up

Draw axial bonds straight Draw equatorial bonds up

up or straight down. and out or down and out.

How not to draw the chair:

H
H H
H H
H H

Incorrect. Incorrect. Incorrect.

Incorrect.
Equatorial bond Axial bond Axial bond should be
Ring should be
should be down should be straight down, equatorial
tilted slightly.
and out. straight up. bond should be up and out.

Aside from drawing the basic chair, the key points are:
Axial bonds alternate up and down, and are shown "vertical".
Equatorial groups are approximately horizontal, but actually somewhat distorted from that (slightly up or slightly down), so that
the angle from the axial group is a bit more than a right angle -- reflecting the common 109.5o bond angle.
Each carbon has an axial and an equatorial bond.
Each face of the cyclohexane ring has three axial and three equatorial bonds.
Each face alternates between axial and equatorial bonds. Then looking at the "up" bond on each carbon in the cyclohexane ring
they will alternate axial-equatorial-axial ect.

4.6.1 https://chem.libretexts.org/@go/page/31413
 When looking down at a cyclohexane ring:
the equatorial bonds will form an "equator" around the ring.
The axial bonds will either face towards you or away. These will alternate with each axial bond. The first axial bond will be
coming towards with the next going away. There will be three of each type.
Note! The terms cis and trans in regards to the stereochemistry of a ring are not directly linked to the terms axial and equatorial.
It is very common to confuse the two. It typically best not to try and directly inter convert the two naming systems.

Axial vs. Equatorial Substituents

When a substituent is added to cyclohexane, the ring flip allows for two distinctly different conformations. One will have the
substituent in the axial position while the other will have the substituent in the equatorial position. In the next section will discuss
the energy differences between these two possible conformations. Below are the two possible chair conformations of
methylcyclohexane created by a ring-flip. Although the conformation which places the methyl group in the equatorial position is
more stable by 7 kJ/mol, the energy provided by ambient temperature allows the two conformations to rapidly interconvert.
CH3
Keq > 1
H
CH3

H
methyl group axial methyl group equatorial
(more stable by 7 kJ/mol)

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 groups to become axial, and vice-versa.
rotate this carbon down

rotate this carbon up

axial
H H UP H H
H H H H
H H H H equatorial
H H H H UP
H H H H
equatorial axial
H H DOWN H H
DOWN

 Example 4.6.1

For the following please indicate if the substituents are in the axial or equatorial positions.
Br Cl

CH3

Solution
Due to the large number of bonds in cyclohexane it is common to only draw in the relevant ones (leaving off the hydrogens
unless they are involved in a reaction or are important for analysis). It is still possible to determine axial and equatorial
positioning with some thought. With problems such as this it is important to remember that each carbon in a cyclohexane ring
has one axial and one equatorial bond. Also, remember that axial bonds are perpendicular with the ring and appear to be going
either straight up or straight down. Equatorial bonds will be roughly in the plane of the cyclohexane ring (only slightly up or
down). Sometimes it is valuable to draw in the additional bonds on the carbons of interest.
H H

Br Cl
H

CH3

4.6.2 https://chem.libretexts.org/@go/page/31413
 With this it can be concluded that the bromine and chlorine substituents are attached in equatorial positions and the CH3
substituent is attached in an axial position.

Exercises
1) Draw two conformations of cyclohexyl amine (C6H11NH2). Indicate axial and equatorial positions.
2) Draw the two isomers of 1,4-dihydroxylcyclohexane, identify which are equatorial and axial.
3) In the following molecule, label which are equatorial and which are axial, then draw the chair flip (showing labels 1,2,3).

Solutions
1)

2)

3) Original conformation: 1 = axial, 2 = equatorial, 3 = axial

Flipped chair now looks like this.

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.

4.6.3 https://chem.libretexts.org/@go/page/31413
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.

4.6: Axial and Equatorial Bonds in Cyclohexane is shared under a CC BY-SA 4.0 license and was authored, remixed, and/or curated by Steven
Farmer, Dietmar Kennepohl, Layne Morsch, Krista Cunningham, Tim Soderberg, Kelly Matthews, & Kelly Matthews.

4.6.4 https://chem.libretexts.org/@go/page/31413
4.7: 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.
H CH3 CH3
H H H3 C H
H H H H
H H H
methylcyclohexane n-butane

Newman projections of methylcyclohexane and n‑butane

When a substituent is added to a cyclohexane ring, the two possible chair conformations created during a ring flip are not equally
stable. In the example of methylcyclohexane the conformation where the methyl group is in the equatorial position is more stable
than the axial conformation by 7.6 kJ/mol at 25o C. The percentages of the two different conformations at equilibrium can be
determined by solving the following equation for K (the equilibrium constant): ΔE = -RTlnK. In this equation ΔE is the energy
difference between the two conformations, R is the gas constant (8.314 J/mol•K), T is the temperature in Kelvin, and K is the
equilibrium constant for the ring flip conversion. Using this equation, we can calculate a K value of 21 which means about 95%
methylcyclohexane molecules have the methyl group in the equatorial position at 25o C.
CH3
Keq > 1
H
CH3

H
methyl group axial methyl group equatorial
(more stable by 7 kJ/mol)

The energy difference between the two conformations comes from strain, called 1,3-diaxial interactions, created when the axial
methyl group experiences steric crowding with the two axial hydrogens located on the same side of the cyclohexane ring. Because
axial bonds are parallel to each other, substituents larger than hydrogen experience greater steric crowding when they are oriented
axial rather than equatorial. Consequently, substituted cyclohexanes will preferentially adopt conformations in which the larger
substituents are in the equatorial orientation. When the methyl group is in the equatorial position this strain is not present which
makes the equatorial conformer more stable and favored in the ring flip equilibrium.
steric repulsion H
H
H C
5 H H 1

6
H
3
4 2

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Actually, 1,3-diaxial steric strain is directly related to the steric strain created in the gauche conformer of butane discussed in
Section: 3-7. When butane is in the gauche conformation 3.8 kJ/mol of strain was created due the steric crowding of two methyl
group with a 60o dihedral angle. When looking at the a Newman projection of axial methylcyclohexane the methyl group is at a 60o
dihedral angle with the ring carbon in the rear. This creates roughly the same amount of steric strain as the gauche conformer of
butante. Given that there is actually two such interactions in axial methylcyclohexane, it makes sense that there is 2(3.8 kJ/mol) =
7.6 kJ/mol of steric strain in this conformation. The Newman projection of equatorial methylcyclohexane shows no such
interactions and is therefore more stable.
H CH3 CH3
H H H3 C H
H H H H
H H H
methylcyclohexane n-butane

Newman projections of methyl cyclohexane and butane showing similarity of 1,3-diaxial and gauche interactions.
Strain values for other cyclohexane substituents can also be considered. The relative steric hindrance experienced by different
substituent groups oriented in an axial versus equatorial location on cyclohexane determined the amount of strain generated. The
strain generated can be used to evaluate the relative tendency of substituents to exist in an equatorial or axial location. Looking at
the energy values in this table, it is clear that as the size of the substituent increases, the 1,3-diaxial energy tends to increase, also.
Note that it is the size and not the molecular weight of the group that is important. Table 4.7.1 summarizes some of these strain
values values.
Table 4.7.1: A Selection of ΔG° Values for the Change from Axial to Equatorial Orientation of Substituents for Monosubstituted
Cyclohexanes
Substituent -ΔG° (kcal/mol) Substituent -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 HO C−
2
0.7

F− 0.3 H C=CH−
2
1.3

Cl− 0.5 C H −
6 5
3.0

Br− 0.5

I− 0.5

Exercises
1) In the molecule, cyclohexyl ethyne there is little steric strain, why?

2) Calculate the energy difference between the axial and equatorial conformations of bromocyclohexane?
3) Using your answer from Question 2) estimate the percentages of axial and equatorial conformations of bromocyclohexane at 25o
C.

4.7.2 https://chem.libretexts.org/@go/page/31414
4) There very little in 1,3-diaxial strain when going from a methyl substituent (3.8 kJ/mol) to an ethyl substituent (4.0 kJ/mol),
why? It may help to use molecular model to answer this question.

Solutions
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.

2) The equatorial conformation of bromocyclohexane will have two 1,3 diaxial interactions. The table above states that each
interaction accounts for 1.2 kJ/mol of strain. The total strain in equatorial bromocyclohexane will be 2(1.2 kJ/mol) = 2.4 kJ/mol.
3) Remembering that the axial conformation is higher in energy, the energy difference between the two conformations is ΔE = (E
equatorial - E axial) = (0 - 2.4 kJ/mol) = -2.4 kJ/mol. After converting oC to Kelvin and kJ/mol to J/mol we can use the equation
ΔE = -RT lnK to find that -ΔE/RT = lnK or (2.4 x 103 J/mol) / (8.313 kJ/mol K • 298 K) = lnK. From this we calculate that K = 2.6.
Because the ring flip reaction is an equilibrium we can say that K = [Equatorial] / [Axial]. If assumption is made that [Equatorial] =
X then [Axial] must be 1-X. Plugging these values into the equilibrium expression produces K = [X] / [1-X]. After plugging in the
calculated value for K, X can be solved algebraically. 2.6 = [X] / [1-X] → 2.6 - 2.6X = X → 2.6 = 3.6X → 2.6/3.6 = X = 0.72. This
means that bromocyclohexane is in the equatorial position 72% of the time and in the axial position 28% of the time.

4) The fact that C-C sigma bonds can freely rotate allows the ethyl subsistent to obtain a conformation which places the bulky CH3
group away from the cyclohexane ring. This forces the ethyl substituent to have only have 1,3- diaxial interactions between
hydrogens, which only provides a slight difference to a methyl group.

Exercises
Questions
Q4.7.1
In the molecule, cyclohexyl ethyne there is little steric strain, why?
Solutions
S4.7.1

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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.

4.7: Conformations of Monosubstituted Cyclohexanes is shared under a CC BY-SA 4.0 license and was authored, remixed, and/or curated by
Steven Farmer, Dietmar Kennepohl, Layne Morsch, Krista Cunningham, Tim Soderberg, Robert Bruner, & Robert Bruner.

4.7.4 https://chem.libretexts.org/@go/page/31414
4.8: 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 conformation in which both substituents are equatorial will always be more stable than a conformation with both groups
axial.
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
In the previous section, it was stated that the chair conformation in which the methyl group is equatorial is more stable because it
minimizes steric repulsion, and thus the equilibrium favors the more stable conformer. This is true for all monosubstituted
cyclohexanes. The chair conformation which places the substituent in the equatorial position will be the most stable and be favored
in the ring flip equilibrium.
CH3
Keq > 1
H
CH3

H
methyl group axial methyl group equatorial
(more stable by 7 kJ/mol)

steric repulsion H
H
H C
5 H H 1

6
H
3
4 2

Disubstituted Cyclohexanes
Determining the more stable chair conformation becomes more complex when there are two or more substituents attached to the
cyclohexane ring. To determine the stable chair conformation, the steric effects of each substituent, along with any additional steric
interactions, must be taken into account for both chair conformations.
In this section, the effect of conformations on the relative stability of disubstituted cyclohexanes is examined using the two
principles:
i. Substituents prefer equatorial rather than axial positions in order to minimize the steric strain created of 1,3-diaxial interactions.
ii. The more stable conformation will place the larger substituent in the equatorial position.

1,1-Disubstituted Cyclohexanes
The more stable chair conformation can often be determined empirically or by using the energy values of steric interactions
previously discussed in this chapter. Note, in some cases there is no discernable energy difference between the two chair

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conformations which means they are equally stable.
1,1-dimethylcyclohexane does not have cis or trans isomers, because both methyl groups are on the same ring carbon. Both chair
conformers have one methyl group in an axial position and one methyl group in an equatorial position giving both the same relative
stability. The steric strain created by the 1,3-diaxial interactions of a methyl group in an axial position (versus equatorial) is 7.6
kJ/mol (from Table 4.7.1), so both conformers will have equal amounts of steric strain. Thus, the equilibrium between the two
conformers does not favor one or the other. Note, that both methyl groups cannot be equatorial at the same time without breaking
bonds and creating a different molecule.
CH3
CH3

1,1-dimethylcyclohexane
1,3-diaxial interactions (7.6 kJ/mol)

H CH3 H
H
H CH3 H CH3
H
H H CH3
1,3-diaxial interactions (7.6 kJ/mol)

However, if the two groups are different, as in 1-tert-butyl-1-methylcyclohexane, then the equilibrium favors the conformer in
which the larger group (tert-butyl in this case) is in the more stable equatorial position. The energy cost of having one tert-butyl
group axial (versus equatorial) can be calculated from the values in table 4.7.1 and is approximately 22.8 kJ/mol. The conformer
with the tert-butyl group axial is approximately 15.2 kJ/mol (22.8 kJ/mol - 7.6 kJ/mol) less stable then the conformer with the tert-
butyl group equatorial. Solving for the equilibrium constant K shows that the equatorial is preferred about 460:1 over axial. This
means that 1-tert-butyl-1-methylcyclohexane will spend the majority of its time in the more stable conformation, with the tert-butyl
group in the equatorial position.
C(CH3)3
CH3

1-(tert-butyl)-1-methylcyclohexane
1,3-diaxial interactions (22.8 kJ/mol)

H C(CH3)3 H
H
H CH3 H C(CH3)3
H
H H CH3
1,3-diaxial interactions (7.6 kJ/mol)

Cis and trans stereoisomers of 1,2-dimethylcyclohexane

In cis-1,2-dimethylcyclohexane, both chair conformations have one methyl group equatorial and one methyl group axial. As
previously discussed, the axial methyl group creates 7.6 kJ/mol of steric strain due to 1,3-diaxial interactions. It is important to
note, that both chair conformations also have an additional 3.8 kJ/mol of steric strain created by a gauche interaction between the
two methyl groups. Overall, both chair conformations have 11.4 kJ/mol of steric strain and are of equal stability.
CH3

CH3
cis -1,2-dimethylcyclohexane
gauche
CH3
1,3-diaxial + gauche interactions (11.4 kJ/mol) CH3
H H ring CH3
H CH3 HH C gauche CH3
3 ring H
H H gauche H
H CH3
H CH3
1,3-diaxial + gauche interactions (11.4 kJ/mol)

In trans-1,2-dimethylcyclohexane, one chair conformer has both methyl groups axial and the other conformer has both methyl
groups equatorial. The conformer with both methyl groups equatorial has no 1,3-diaxial interactions however there is till 3.8 kJ/mol
of strain created by a gauche interaction. The conformer with both methyl groups axial has four 1,3-Diaxial interactions which
creates 2 x 7.6 kJ/mol (15.2 kJ/mol) of steric strain. This conformer is (15.2 kJ/mol -3.8 kJ/mol) 11.4 kJ/mol less stable than the
other conformer. The equilibrium will therefore favor the conformer with both methyl groups in the equatorial position.

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 CH3

CH3
trans -1,2-dimethylcyclohexane

two 1,3-diaxial interactions (15.2 kJ/mol)

H CH3 H
H H H H H
H CH3 ring CH3
H H gauche
CH3 gauche H CH3
H ring CH3
H CH3 CH3 H
gauche interaction (3.8 kJ/mol)

Cis and trans stereoisomers of 1,3-dimethylcyclohexane

A similar conformational analysis can be made for the cis and trans stereoisomers of 1,3-dimethylcyclohexane. For cis-1,3-
dimethylcyclohexane one chair conformation has both methyl groups in axial positions creating 1,3-diaxial interactions. The other
conformer has both methyl groups in equatorial positions thus creating no 1,3-diaxial interaction. Because the methyl groups are
not on adjacent carbons in the cyclohexane rings gauche interactions are not possible. Even without energy calculations it is simple
to determine that the conformer with both methyl groups in the equatorial position will be the more stable conformer.
CH3 CH3
CH3
H 3C CH3

CH3 both methyl groups axial both methyl groups equatorial

1,3-diaxial interactions no interactions
more stable conformer

For trans-1,3-dimethylcyclohexane both conformations have one methyl axial and one methyl group equatorial. Each conformer
has one methyl group creating a 1,3-diaxial interaction so both are of equal stability.
CH3 CH3

CH3
H 3C
CH3 CH3
one methyl group axial one methyl group axial
and one equatorial and one equatorial

both conformers have equal stability

Summary of Disubstitued Cyclohexane Chair Conformations

When considering the conformational analyses discussed above a pattern begins to form. There are only two possible relationships
which can occur between ring-flip chair conformations:
1) AA/EE: One chair conformation places both substituents in axial positions creating 1,3-diaxial interactions. The other conformer
places both substituents in equatorial positions creating no 1,3-diaxial interactions. This diequatorial conformer is the more stable
regardless of the substituents.
2) AE/EA: Each chair conformation places one substituent in the axial position and one substituent in the equatorial position. If the
substituents are the same, there will be equal 1,3-diaxial interactions in both conformers making them equal in stability. However,
if the substituents are different then different 1,3-diaxial interactions will occur. The chair conformation which places the larger
substituent in the equatorial position will be favored.

Substitution type Chair Conformation Relationship

cs-1,2-disubstituted cyclohexanes AE/EA

trans-1,2-disubstituted cyclohexanes AA/EE

cis-1,3-disubstituted cyclohexanes AA/EE

trans-1,3-disubstituted cyclohexanes AE/EA

cis-1,4-disubstituted cyclohexanes AE/EA

trans-1,4-disubstituted cyclohexanes AA/EE

4.8.3 https://chem.libretexts.org/@go/page/31415
  Example 4.8.1
For cis-1-chloro-4-methylcyclohexane, draw the most stable chair conformation and determine the energy difference between
the two chair conformers.

Solution
Based on the table above, cis-1,4-disubstitued cyclohexanes should have two chair conformations each with one substituent
axial and one equatorial. Based on this, we can surmise that the energy difference of the two chair conformations will be based
on the difference in the 1,3-diaxial interactions created by the methyl and chloro substituents.
1,3-diaxial interactions (7.6 kJ/mol)

H CH3 Cl H
H H H H
Cl H H CH3

1,3-diaxial interactions (2.0 kJ/mol)

As predicted, each chair conformer places one of the substituents in the axial position. Because the methyl group is larger and
has a greater 1,3-diaxial interaction than the chloro, the most stable conformer will place it the equatorial position, as shown in
the structure on the right. Using the 1,3-diaxial energy values given in the previous sections we can calculate that the
conformer on the right is (7.6 kJ/mol - 2.0 kJ/mol) 5.6 kJ/mol more stable than the other.

 Example 4.8.2

For trans-1-chloro-2-methylcyclohexane, draw the most stable chair conformation and determine the energy difference
between the two chair conformers.

Solution
Based on the table above, trans-1,2-disubstitued cyclohexanes should have one chair conformation with both substituents axial
and one conformation with both substituents equatorial. Based on this, we can predict that the conformer which places both
substituents equatorial will be the more stable conformer. The energy difference of the two chair conformations will be based
on the 1,3-diaxial interactions created by both the methyl and chloro substituents.
H CH3
H H
H H
H CH3
H Cl
H Cl
both groups are axial both groups are equatorial
1,3-diaxial interactions (9.6 kJ/mol) no 1,3-diaxial interactions

As predicted, one chair conformer places both substituents in the axial position and other places both substituents equatorial.
The more stable conformer will place both substituents in the equatorial position, as shown in the structure on the right. Using
the 1,3-diaxial energy values given in the previous sections we can calculate that the conformer on the right is (7.6 kJ/mol +
2.0 kJ/mol) 9.6 kJ/mol more stable than the other.

Conformational Analysis of Complex Six Membered Ring Structures

Cyclohexane can have more than two substituents. Also, there are multiple six membered rings which contain atoms other than
carbon. All of these systems usually form chair conformations and follow the same steric constraints discussed in this section.
Because the most commonly found rings in nature are six membered, conformational analysis can often help in understanding the
usual shapes of some biologically important molecules. In complex six membered ring structures a direct calculation of 1,3-diaxial
energy values may be difficult. In these cases a determination of the more stable chair conformer can be made by empirically
applying the principles of steric interactions.
A later chapter will discuss how many sugars can exist in cyclic forms which are often six remembered rings. When in an aqueous
solution the six carbon sugar, glucose, is usually a six membered ring adopting a chair conformation. When looking at the two

4.8.4 https://chem.libretexts.org/@go/page/31415
possible ring-clip chair conformations, one has all of the substituents axial and the other has all the substutents equatorial. Even
without a calculation, it is clear that the conformation with all equatorial substituents is the most stable and glucose will most
commonly be found in this conformation.
HO OH
OH
OH Keq >> 1
O HO O
HO OH
OH OH OH

glucose
(β-glucopyranose form)

 Example 4.8.3

The six carbon sugar, fructose, in aqueous solution is also a six-membered ring in a chair conformation. Which of the two
possible chair conformations would be expected to be the most stable?
OH
OH OH
O HO O
OH OH
HO
OH OH
OH
fructose
(β-fructopyranose form)

Solution
The lower energy chair conformation is the one with three of the five substituents (including the bulky –CH2OH group) in the
equatorial position (pictured on the right). The left structure has 3 equatorial substituents while the structure on the right only
has two equatorial substituents.

Exercises
1. Draw the two chair conformations for cis-1-ethyl-2-methylcyclohexane using bond-line structures and indicate the more
energetically favored conformation.
2. Draw the most stable conformation for trans-1-ethyl-3-methylcyclohexane using bond-line structures.
3. Draw the most stable conformation for trans-1-t-butyl-4-methylcyclohexane using bond-line structures.
4. Draw the most stable conformation fo trans-1-isopropyl-3-methylcyclohexane.
5. Can a ‘ring flip’ change a cis-disubstituted cyclohexane to trans? Explain.
6. Draw the two chair conformations of the six-carbon sugar mannose, being sure to clearly show each non-hydrogen substituent as
axial or equatorial. Predict which conformation is likely to be more stable, and explain why.

Solutions

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4.

The bulkier isopropyl groups is in the equatorial position.

5. No. In order to change the relationship of two substituents on a ring from cis to trans, you would need to break and reform two
covalent bonds. Ring flips involve only rotation of single bonds.
6.

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 equatorial reducing steric interaction
2 – The most stable conformation would be to have the groups equatorial this would reduce the strain if they were axial

4.8: Conformations of Disubstituted Cyclohexanes is shared under a CC BY-SA 4.0 license and was authored, remixed, and/or curated by Jim
Clark, Steven Farmer, Dietmar Kennepohl, Layne Morsch, Krista Cunningham, Tim Soderberg, Kelly Matthews, Robert Bruner, & Robert
Bruner.

4.8.6 https://chem.libretexts.org/@go/page/31415
4.9: Conformations of Polycyclic Molecules
 Objective

After completing this section, you should be able to draw the structures and construct molecular models of simple polycyclic
molecules.

 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.

Nomenclature of Bicyclic Ring Systems

There are many hydrocarbons and hydrocarbon derivatives with two rings having common carbon atoms. There are three main ways that
the two rings can be connected. The first is called a fused bicyclic ring structure where the two rings share a covalent bond and a have two
bridgehead carbons (marked in red on the structures below). A bridgehead is defined as a carbon that is part of two or more rings.
Hydrogens attached to bridge head carbons are often referred to as bridge head hydrogens. The two rings can also be connected by a bridge
containing one or more carbons to form a bridged bicyclic molecule. Lastly, the two rings can be joined with a singe bridge head carbon to
form spiro bicyclic molecules.

fused bridged spiro

= bridgehead carbons

Bicyclic Isomers of C10H18

Naming Fused and Bridged Compounds

Fused and bridged bicyclic compounds are follow similar naming conventions:
1. Count the total number of carbons in both rings. This is the parent name. (eg. ten carbons in the system would be decane)
2. Count the number of carbons between the bridgeheads, then place the numbers in square brackets in descending order separated by
periods. Fused and bridged bycyclic compounds should have three numbers such as [2.2.0]. For fused compounds one of the numbers
should be zero.
3. Place the word bicyclo at the beginning of the name.
1 1 1
1 2
2 2
0 2 1
3 3
3 3
4 4 4

bicyclo[4.4.0]decane bicyclo[4.3.1]decane

Examples with carbons and hydrogens explicitly shown:

H
H C H
C H 2C CH2 C
H 2C CH2 H 2C H 2C CH2
CH2 H 2C CH C
H 2C CH2 C H
H2
bicyclo[2.2.1]heptane bicyclo[3.1.1]heptane bicyclo[1.1.0]butane

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Naming Spiro Compounds
Spiro bicyclics are named using the same basic rules. Because there is only one bridgehead carbon only two numbers will be required in the
brackets. Also, the word spiro is placed at the beginning.
2 1 1
2
3
3
4 5 4

spiro[5.4]decane

Examples

spiro[4.4]nonane spiro[3.2]hexane

Conformations in Bicyclic Ring Systems

As expected, the connection of two rings has defined effects on the possible conformations. However, the ideas previously discussed in this
chapter can be used for conformational analysis. Fused rings have the possibility of two isomers where the bridgehead hydrogens are either
cis or trans along the shared bond. These two isomers have significant differences in flexibility and stability as seen in bicyclo[4,4,0]decane
more commonly known as decalin. If the positioning of the bridgehead hydrogens are shown in a fused ring the prefix cis or trans should be
included in the name.
The trans-isomer is the easiest to describe because the fusion of the two rings creates a rigid, roughly planar, structure made up of two chair
conformations. Unlike cyclohexane, the two rings cannot flip from one chair form to another. Accordingly, the orientation of the any
substituents is fixed in either an axial or equatorial position in trans-decalin. This means that the C-C bonds coming away from the fused
edge are held in equatorial positions relative to each ring thus preventing the possibility of any 1,3-diaxial interactions occurring between
ring atoms.
H H

H H
trans -decalin
(rigid)

2kcal mol&#x2212;1" id="MathJax-Element-1-Frame" role="presentation" style="position:relative;" tabindex="0">

The two rings in cis-decalin are also both held in a chair conformations. In comparison, the chair-chair forms of cis-decalin are relatively
flexible, and inversion of both rings at once occurs fairly easily.
H H H
H
H

H
cis -decalin
(more flexible)

The flexibility of cis-decalin allows for a substituent to interconvert between axial and equatorial conformations. In much the same fashion
as cyclohexane, equatorial substituents tend to create less steric strain and create a more stable conformer.
CH3 CH3
2 3 4
1 3
2
1 6 5
6 5 4

(Note: atoms are mapped in blue for clarity.)

A major difference in cis-decalin is the fact that one of C-C bonds coming away from the fused edge is held an an axial position. This is true
in both ring-flip conformations. This axial C-C bond causes 1,3-diaxial interactions to occur in cis-decalin making it roughly 8.4 kJ/mol less
stable than trans-decalin. This amount of 1,3-diaxial steric strain is roughly equivalent to that of an ethyl substituent attached to a
cyclohexane ring (8.0 kJ/mol)

H H
H H

= steric strain

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Bicyclic compounds with a bridge typically have very little flexibility and are often held in a ridged conformation. The molecule
norbornane represent a cyclohexane ring connected by a single carbon bridge.

norbornane, or
bicyclo[2.2.1]heptane

Norbornane is estimated to have 72 kJ/mol of ring strain which can be understood when viewing the contained rings. The carbon bridge in
norbornane holds the cyclohexane ring at the bottom in a boat conformation creating torsional strain from eclipsing bonds along the edge.

H H
H H
H H
H H
(green arrows used to illustrate
eclipsing hydrogens)

Also, the carbon bridge forms a cyclopentane ring (shown in red below making up the right side of the structure) with increased angle strain
throughout the whole molecule.

Polycyclic Systems in Nature

Fused ring systems like decalin are very common in natural products. In fact, similar ring systems are found in steroids, which are an
important class of lipids. Steroids generally have structures that include three six-membered rings and a five-membered ring connected by
three fused bonds. Most natural steroids have a trans configuration at all three fusion points. This tends to give steroids a rigid and semi-flat
structure.
H
H H

H H
H

basic steroid ring confguration trans-trans-trans

(fused bonds highlighted in purple)

Sex hormones are an example of 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 and is synthesized from cholesterol in the testes. It also promotes secondary male sexual
characteristics such as deep voice, facial and body hair.
OH OH

H H

H H H H
O HO
testosterone estradiol

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.

H H
HO
cholesterol

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Exercises
1)

i)

j)

3) The following molecule is cholic acid. Determine if the three fused bonds have a cis or trans configuration.

Solutions
1)
a) Bicyclo[2.1.1]hexane
b) Bicyclo[3.2.1]octane
c) Bicyclo[2.1.0]pentane (more commonly called "housane")
d) Bicyclo[2.2.2]octane
e) cis-Bicyclo[3.3.0]octane
f) cis-Bicyclo[1.1.0]butane
g) Bicyclo[1.1.1]pentane
h) Bicyclo[4.3.3]dodecane
i) Spiro[5.2]octane
j) Spiro[3.3]heptane
2)

4.9.4 https://chem.libretexts.org/@go/page/31416
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.

4.9: Conformations of Polycyclic Molecules is shared under a CC BY-SA 4.0 license and was authored, remixed, and/or curated by Chris Schaller, Steven
Farmer, Dietmar Kennepohl, Layne Morsch, Krista Cunningham, Gamini Gunawardena, Marjorie C. Caserio, & Marjorie C. Caserio.

4.9.5 https://chem.libretexts.org/@go/page/31416
4.S: Organic Compounds- Cycloalkanes and their Stereochemistry (Summary)
Concepts & Vocabulary
4.1: Naming Cycloalkanes
Cycloalkanes are saturated hydrocarbons that have the generic formula CnH2n , where n is the number of carbons in the ring.
The IUPAC rules for naming cycloalkanes is very similar to the rules used for naming alkanes.
4.2: Cis-Trans Isomerism in Cycloalkanes
Stereoisomers are molecules that have the same molecular formula, the same atom connectivity, but they differ in the relative
spatial orientation of the atoms.
Di-substituted cycloalkanes exhibit cis- / trans- stereoisomerism. The cis- isomer has both substituents on the same face of the
ring, while the trans- isomer has groups on opposite faces of the ring.
4.3: Stability of Cycloalkanes - Ring Strain
Ring strain is the total strain in a ring due to torsional strain, steric strain and angle strain.
Angle strain is when the C-C-C bond angles in rings are different than 109.5o, the optimal bond angle for sp3 hybridized
carbons.
Ring strain causes small cycloalkanes, like cyclopropane and cyclobutane, to be much less stable than other cycloalkanes.
4.4: Conformations of Cycloalkanes
Cyclopentane has less ring strain than cyclopropane and cyclobutane, because its ring carbons have more flexibility to rotate
away from planarity, resulting in lower angle and torsional strains.
4.5: Conformations of Cyclohexane
Cyclohexane has significantly lower ring strain than smaller cycloalkanes, because cyclohexane can adopt non-planar
structures, which minimize angle strain and torsional strain.
The common non-planar structures of cyclohexane are the boat, twist-boat, and chair conformations. The most stable, and
hence, the most common, is the chair conformation.
4.6: Axial and Equatorial Bonds in Cyclohexane
The two chair conformations of cyclohexane interconvert rapidly at room temperature in a process called chair flip or ring flip.
In the chair conformation of cyclohexane, of the two groups attached to each ring carbon, one of the groups occupies the axial
position, while the other group occupies the equatorial position.
A group that was axial will switch to the equatorial position during a ring flip, and vice versa.
4.7: Conformations of Monosubstituted Cyclohexanes
To minimize the steric effects of 1,3-diaxial interactions, the single group on a monosubstituted cyclohexane ring will prefer to
be in the equatorial position over the axial position. The larger the group, the greater is the preference shifts.
4.8: Conformations of Disubstituted Cyclohexanes
The preference for large groups to be in the equatorial position effects the relative stability of the cis and trans isomers of
disubstituted cyclohexanes. Conformational analysis is the process used to determine which isomer, cis or trans, is most
stable.
4.9: Conformations of Polycyclic Molecules

Summary Problems

 Exercise 4.S. 1
The following molecule, quinic acid, is a natural product that can be obtained from a variety of sources including the coffee
bean. Draw both chair conformations for this molecule, identify each substituent in both structures as axial or equatorial, and
clearly indicate which chair conformation is the most stable.

4.S.1 https://chem.libretexts.org/@go/page/169605
 OH
HO OH

HO OH
O

Answer
equatorial
axial axial
HO axial OH
OH OH
OH equatorial
HO OH equatorial
OH equatorial HO
axial
O equatorial O OH
axial

The circled conformation is more stable because it has more equatorial substituents (3 versus 2) and the largest group (the
carboxylic acid) is equatorial.

 Exercise 4.S. 2

Convert the following name to a skeletal structure: cis-1-t-butyl-2-ethylcyclohexane. Then, draw this molecule in a chair
conformation and perform a ring flip. Circle the most stable of the two conformations.

Answer

Remember that, due to its large size, the t-butyl substituent locks the cyclohexane ring into one conformation with the t-
butyl in the equatorial position. Thus, this isn't an equilibrium. It exists only as the circled conformation.

 Exercise 4.S. 3

Convert the following name to a skeletal structure: trans-3-isobutylcyclohexanol. Then, draw the two chair conformations,
label substituents as axial or equatorial, and circle the more stable conformation.

Answer
OH

axial
OH
OH
equatorial
equatorial
axial

The circled molecule is most stable because the larger substituent is equatorial.

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Skills to Master
Skill 4.1 Be able to name and draw cycloalkanes
Skill 4.2 Identify and draw the cis- and trans- stereoisomers of disubstituted cycloalkanes.
Skill 4.3 Determine the effects of torsional strain, steric strain, and angle strain on the overall ring strain of a cycloalkane.
Skill 4.4 Draw the chair conformers of cyclohexane.
Skill 4.5 Draw and identify the axial and equatorial positions in a chair conformer of cyclohexane and its ring-flip conformer.
Skill 4.6 Use conformational analysis to determine the most stable stereoisomer in disubstituted and polysubstituted
cyclohexanes.

Contributors
Dr. Kelly Matthews, Harrisburg Area Community College
Kevin M. Shea (Smith College)

4.S: Organic Compounds- Cycloalkanes and their Stereochemistry (Summary) is shared under a CC BY-SA 4.0 license and was authored,
remixed, and/or curated by Kelly Matthews & Kevin M. Shea.

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 CHAPTER OVERVIEW
5: Stereochemistry at Tetrahedral Centers
 Learning Objectives

After you have completed Chapter 5, you should be able to

fulfill all of the detailed objectives listed under each individual section.
use molecular models in solving problems on stereochemistry.
solve road-map problems that include stereochemical information.
define, and use in context, the new key terms.

This chapter introduces the concept of chirality, and discusses the structure of compounds containing one or two chiral centers. A
convenient method of representing the three-dimensional arrangement of the atoms in chiral compounds is explained; furthermore,
throughout the chapter , considerable emphasis is placed on the use of molecular models to assist in the understanding of the
phenomenon of chirality. The chapter continues with an examination of stereochemistry—the three-dimensional nature of
molecules. The subject is introduced using the experimental observation that certain substances have the ability to rotate plane-
polarized light. Finally, certain reactions of alkenes are re-examined in the light of the new material encountered in this chapter.
5.0: Chapter Objectives and Introduction
5.1: Enantiomers and the Tetrahedral Carbon
5.2: The Reason for Handedness in Molecules - Chirality
5.3: Optical Activity
5.4: Pasteur's Discovery of Enantiomers
5.5: Sequence Rules for Specifying Configuration
5.6: Diastereomers
5.7: Meso Compounds
5.8: Racemic Mixtures and the Resolution of Enantiomers
5.9: A Review of Isomerism
5.10: Chirality at Nitrogen, Phosphorus, and Sulfur
5.11: Prochirality
5.12: Chirality in Nature and Chiral Environments
5.S: Stereochemistry at Tetrahedral Centers (Summary)
5.xx: Enantiomers and Diastereomers

5: Stereochemistry at Tetrahedral Centers is shared under a CC BY-SA 4.0 license and was authored, remixed, and/or curated by Dietmar
Kennepohl.

1
5.0: Chapter Objectives and Introduction
The opposite of chiral is achiral. Achiral objects are superimposable with their mirror images. If the molecules are superimposable,
they are identical to each other. For example, two pieces of paper are achiral. In contrast, chiral objects, 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?

O O O O

aS aR

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. This pair of non-superimposable mirror image molecules are called enantiomers. But why are
chiral molecules so interesting? 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, as the other. It turns out that many of the biological molecules such as our
DNA, amino acids and sugars, are chiral molecules.

5.0: Chapter Objectives and Introduction is shared under a CC BY-SA 4.0 license and was authored, remixed, and/or curated by Steven Farmer,
Dietmar Kennepohl, Krista Cunningham, & Krista Cunningham.

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5.1: 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 the most
interesting types of isomer is the mirror-image stereoisomer, a non-superimposable set of two molecules that are mirror images
of one another. The existence of these molecules are determined by a a concept known as chirality. The word “chiral” was
derived from the Greek word for hand, because our hands are a good example of chirality since they are non-superimposable
mirror images of each other.

Chiral Molecules
The term chiral, from the Greek work for 'hand', refers to anything which cannot be superimposed on its own mirror image.
Certain organic molecules are chiral meaning that they are not superimposable on their mirror image. Chiral molecules contain one
or more chiral centers, which are almost always tetrahedral (sp3-hybridized) carbons with four different substituents. Consider the
molecule A below: a tetrahedral carbon, with four different substituents denoted by balls of four different colors.
mirror plane

C C

A B

The mirror image of A, which we will call B, is drawn on the right side of the figure, and an imaginary mirror is in the middle.
Notice that every point on A lines up through the mirror with the same point on B: in other words, if A looked in the mirror, it
would see B looking back.
Now, if we flip compound A over and try to superimpose it point for point on compound B, we find that we cannot do it: if we
superimpose any two colored balls, then the other two are misaligned.

5.1.1 https://chem.libretexts.org/@go/page/31420
 mirror plane

C C

C
A B
C

flip A over so
that red item
points to the left A and B cannot be superimposed.
They are not the same molecule!
C

A is not superimposable on its mirror image (B), thus by definition A is a chiral molecule. It follows that B also is not
superimposable on its mirror image (A), and thus it is also a chiral molecule.
A and B are called stereoisomers or optical isomers: molecules with the same molecular formula and the same bonding
arrangement, but a different arrangement of atoms in space. Enantiomers are pairs of stereoisomers which are mirror images of
each other: thus, A and B are enantiomers. It should be self-evident that a chiral molecule will always have one (and only one)
enantiomer: enantiomers come in pairs. Enantiomers have identical physical properties (melting point, boiling point, density, and so
on). However, enantiomers do differ in how they interact with polarized light (we will learn more about this soon) and they may
also interact in very different ways with other chiral molecules - proteins, for example. We will begin to explore this last idea in
later in this chapter, and see many examples throughout the remainder of our study of biological organic chemistry.

 The Many Synonyms of the Chiral Carbon

Be aware - all of the following terms can be used to describe a chiral carbon.
chiral carbon = asymmetric carbon = optically active carbon = stereo carbon = stereo center = chiral center

Let's apply our chirality discussion to real molecules.

Consider 2-butanol, drawn in two dimensions below.
3 4 4
CH2CH3
2 3 OH
H C OH = 2
=
OH
1
CH3 1

2-butanol
(drawn in 2D)

Carbon #2 is a chiral center: it is sp3-hybridized and tetrahedral (even though it is not drawn that way above), and the four
substituents attached to is are different: a hydrogen (H) , a methyl (-CH3) group, an ethyl (-CH2CH3) group, and a hydroxyl (OH)
group. If the bonding at C2 of 2-butanol is drawn in three dimensions and this structure called A. Then the mirror image of A can
be drawn to form structure B.
mirror plane

CH2CH3 CH2CH3
C = =
H C OH HO
C H C
H 3C CH3
A B

flip A over so
that OH points CH2CH3
to the left
C CH =
HO H
3 C
A

A and B cannot be superimposed.

They are both chiral and are
enantiomers!

When we try to superimpose A onto B, we find that we cannot do it. Because structure A and B are not superimposable on their
mirror image they are both chiral molecules. Because A and B are different due only to the arrangement of atoms in space they are

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stereoisomers. Because A and B are mirror images of each other they are also enantiomers. When looking at simplified line
structures is clear that there are two distinct ways of drawing 2-butanol which only differ in their spatial arrangement around a
chiral carbon.
HO H HO H

two enantiomers of 2-butanol

5.1.3 https://chem.libretexts.org/@go/page/31420
 GLmol

GLmol
The 3D Structures of the Two Enantiomers of 2-Butanol
For comparison, 2-propanol, is an achiral molecule because is lacks a chiral carbon. Carbon #2 is bonded to two identical
substituents (methyl groups), and so it is not a chiral carbon. Being achiral means that 2-propanol should be superimposable on its

5.1.4 https://chem.libretexts.org/@go/page/31420
mirror image which is shown in the figure below. A more detailed explaination on why 2-propanol is achiral will be given in the
next section.
2-propanol is achiral:
mirror plane

CH3 CH3

H C CH H3 C
C H
H3 C 3 CH3
C D

tip C on its side

CH3
C H
H3 C CH3
C
C and D can be superimposed.
They are the same molecule!

Stereoisomers
Stereoisomers have been defined as molecules with the same connectivity but different arrangements of the atoms in space. It is
important to note that there are two types of stereoisomers: geometric and optical.
Optical isomers are molecules whose structures are mirror images but cannot be superimposed on one another in any orientation.
Optical isomers have identical physical properties, although their chemical properties may differ in asymmetric environments.
Molecules that are nonsuperimposable mirror images of each other are said to be chiral.
25.7.1a" id="MathJax-Element-1-Frame" role="presentation" style="position:relative;" tabindex="0">
Geometric isomers differ in the relative position(s) of substituents in a rigid molecule. Simple rotation about a C–C σ bond in an
alkene, for example, cannot occur because of the presence of the π bond. The substituents are therefore rigidly locked into a
particular spatial arrangement. Thus a carbon–carbon multiple bond, or in some cases a ring, prevents one geometric isomer from
being readily converted to the other. The members of an isomeric pair are identified as either cis or trans, and interconversion
between the two forms requires breaking and reforming one or more bonds. Because their structural difference causes them to have
different physical and chemical properties, cis and trans isomers are actually two distinct chemical compounds.mers have the same
connectivity, but different arrangements of atoms in space. Geometric isomers will be discussed in more detain in Sections 7.4 and
7.5.

 Exercise 5.1.1

Identify the following molecules as chiral or achiral.

Br H3 C H3CH2C
a) H b) CH3 c) OH
F I F I H3CH2C I

d) e) f)

OH OH

Answer
a) chiral (4 different groups off C)
b) achiral (2 identical -CH3 substituents off central C)
c) achiral (2 identical -CH2CH3 substituents off central C)
d) achiral (2 identical CH3 substituents off carbon 2)
e) chiral (4 different groups off carbon 2)
f) achiral (2 identical CH3 substituents off central C)

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  Exercise 5.1.2

Determine if the following sets of compounds in each group are enantiomers or the same compound.
Br Br
a) OH & H
Cl H Cl OH

Br H
b) OH Br
&
Cl H Cl OH

c) H Br
Cl & H
HO Br Cl OH

d)
&

OH OH

Answer
a) enantiomers – non superimposable mirror images
b) same compound – when you rotate the molecule on the right it is identical to the one on the left
c) enantiomers – non superimposable mirror images
d) enantiomers – non superimposable mirror images

5.1: Enantiomers and the Tetrahedral Carbon is shared under a CC BY-SA 4.0 license and was authored, remixed, and/or curated by Jim Clark,
Steven Farmer, Dietmar Kennepohl, Zachary Sharrett, Krista Cunningham, Tim Soderberg, William Reusch, & William Reusch.
Current page by Dietmar Kennepohl, Jim Clark, Krista Cunningham, Steven Farmer, Tim Soderberg, William Reusch, Zachary Sharrett is
licensed CC BY-SA 4.0.
3.4: Chirality and stereoisomers by Tim Soderberg is licensed CC BY-NC-SA 4.0. Original source:
https://digitalcommons.morris.umn.edu/chem_facpubs/1/.
24.7: Chirality in Organic Chemistry is licensed CC BY-NC-SA 3.0.

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5.2: 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

Symmetry and Chirality

Molecules that are nonsuperimposable mirror images of each other are said to be chiral (pronounced “ky-ral,” from the Greek cheir,
meaning “hand”). Examples of some familiar chiral objects are your hands. Your left and right hands are nonsuperimposable mirror
images. (Try putting your right shoe on your left foot—it just doesn’t work.) An achiral object is one that can be superimposed on
its mirror image, as shown by the superimposed flasks 25.7.1b in the figure below. .

An an important questions is why is one chiral and the other not? The answer is that the flask has a plane of symmetry and your
hand does not. A plane of symmetry is a plane or a line through an object which divides the object into two halves that are mirror
images of each other. When looking at the flask, a line can be drawn down the middle which separates it into two mirror image
halves. However, a similar line down the middle of a hand separates it into two non-mirror image halves. This idea can be used to
predict chirality. If an object or molecule has a plane of symmetry it is achiral. If if lacks a plane of symmetry it is chiral.

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Symmetry can be used to explain why a carbon bonded to four different substituents is chiral. When a carbon is bonded to fewer
than four different substituents it will have a plane of symmetry making it achiral. A carbon atom that is bonded to four different
substituents loses all symmetry, and is often referred to as an asymmetric carbon. The lack of a plane of symmetry makes the
carbon chiral. The presence of a single chiral carbon atom sufficient to render the molecule chiral, and modern terminology refers
to such groupings as chiral centers or stereo centers.
An example is shown in the bromochlorofluoromethane molecule shown in part (a) of the figure below. This carbon, is attached to
four different substituents making it chiral. which is often designated by an asterisk in structural drawings. If the bromine atom is
replaced by another chlorine to make dichlorofluoromethane, as shown in part (b) below, the molecule and its mirror image can
now be superimposed by simple rotation. Thus the carbon is no longer a chiral center. Upon comparison,
bromochlorofluoromethane lacks a plane of symmetry while dichlorofluoromethane has a plane of symmetry.

(a) bromochlorofluoromethane
mirror plane

H H H
180° rotation
Br * * Br Cl *
F F cannot be F
Cl Cl superimposed Br

(b) dichlorofluoromethane

mirror plane

H H H
180° rotation
Cl * * Cl Cl *
F F can be F
Cl Cl superimposed Cl

No Plane of Symmetry Plane of Symmetry

(chiral) (achiral)

H H
Br C Cl Cl C Cl
F F

bromochlorofluoromethane dichlorofluoromethane

Identifying Chiral carbons

Identifying chiral carbons in a molecule is an important skill for organic chemists. The presence of a chiral carbon presents the
possibility of a molecule having multiple stereoisomers. Most of the chiral centers we shall discuss in this chapter are asymmetric
carbon atoms, but it should be recognized that other tetrahedral or pyramidal atoms may become chiral centers if appropriately
substituted. Also, 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. Because an carbon requires four different substituents to become asymmertric, it can be said, with few exceptions, that
sp2 and sp hybridized carbons involved in multiple bonds are achiral. Also, any carbon with more than one hydrogen, such as a -
CH3 or -CH2- group, are also achiral.

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Looking for planes of symmetry in a molecule is useful, but often difficult in practice. 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. 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, the general rule is that molecules
with at least one stereocenter are chiral, and molecules with no stereocenters are achiral.
Determining if a carbon is bonded to four distinctly different substituents can often be difficult to ascertain. Remember even the
slightest difference makes a substituent unique. Often these difference can be distant from the chiral carbon itself. Careful
consideration and often the building of molecular models may be required. A good example is shown below. It may appear that the
molecule is achiral, however, when looking at the groups directly attached to the possible chiral carbon, it is clear that they all
different. The two alkyl groups are differ by a single -CH2- group which is enough to consider them different.
Substituent

H2
C CH3 butyl
C C
H2 H2
H2 HO H H2
C C C CH3 H2
H 3C C * C C C
H2 H2 H2 propyl
C CH3
H2

OH hydroxyl

H hydrogen

 Example 5.2.1

Predict if the following molecule would be chiral or achiral:

CH3

Answer
Achiral. When determining the chirality of a molecule, it best to start by locating any chiral carbons. An obvious candidate
is the ring carbon attached to the methyl substituent. The question then becomes: does the ring as two different substituents
making the substituted ring carbon chiral? With an uncertainty such as this, it is then helpful try to identify any planes of
symmetry in the molecule. This molecule does have a plane of symmetry making the molecule achiral. The plane of
symmetry would be easier see if the molecule were view from above. Typically, monosubstituted cycloalkanes have a
similar plane of symmetry making them all achiral.

 Exercise 5.2.1
Determine if each of the following molecules are chiral or achiral. For chiral molecules indicate any chiral carbons.

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 OH
Br OH

OH
a b c d

Cl Cl H
Cl O

O CH3 O
H
e f g h

Answer

*
Br * OH
* * * *
*
OH
a b c d

Cl Cl H
Cl O
* *
*
O CH3 O
H
e f g h

Explanation
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.

 Note

In the 1960’s, a drug called thalidomide was widely prescribed in the Western Europe to alleviate morning sickness in pregnant
women.
O O H
N
N O

O
thalidomide

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 problem lay in the fact that thalidomide was being provided as a mixture of two different
isomeric forms.
O O H O O H
H N H N
N O N O

O stereocenter O
effective isomer mutagenic isomer

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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. If you make models of the two stereoisomers of thalidomide, you will see that they too are mirror images, and
cannot be superimposed.
σ

O O H H O O
H R3
N N R H
3
R1 N C O O C N R1

R2 R2
O O

C C

As a historical note, thalidomide was never approved for use in the United States. This was thanks in large part to the efforts of
Dr. Frances Kelsey, a Food and Drug officer who, at peril to her career, blocked its approval due to her concerns about the lack
of adequate safety studies, particularly with regard to the drug's ability to enter the bloodstream of a developing fetus.
Unfortunately, though, at that time clinical trials for new drugs involved widespread and unregulated distribution to doctors
and their patients across the country, so families in the U.S. were not spared from the damage caused.
Very recently a close derivative of thalidomide has become legal to prescribe again in the United States, with strict safety
measures enforced, for the treatment of a form of blood cancer called multiple myeloma. In Brazil, thalidomide is used in the
treatment of leprosy - but despite safety measures, children are still being born with thalidomide-related defects.

 Example 5.2.2

Label the molecules below as chiral or achiral, and locate all stereocenters.
a) O b) O
O HO O

O O
O O

fumarate malate
(a citric acid cycle intermediate) (a citric acid cycle intermediate)

c) O OH d) O OH e)
H
N CH3
O O
O
CH3 HO

ibuprofen acetylsalicylic acid acetaminophen

(aspirin) (active ingredient in Tylenol)

Answer
a) O b) O
O HO O

O O
O O

fumarate malate
(achiral) (chiral)

c) O OH d) O OH e)
H
N CH3
O O
O
CH3 HO

ibuprofen acetylsalicylic acid acetaminophen

(chiral) (achiral) (achiral)

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 Exercise 5.2.2

1) For the following compounds, star (*) each chiral center, if any.

2) Explain why the following compound is chiral.

3) Determine which of the following objects is chiral.

a) A Glove.
b) A nail.
c) A pair of sunglasses.
d) The written word "Chiral".
4) Place an "*" by all of the chrial carbons in the following molecules.
a)
Erythrose, a four carbon sugar.

b) Isoflurane, an anestetic. Bright green = Chlorine, Pale green = Fluorine.

Answer
1)

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 2) Though the molecule does not contain a chiral carbon, it is chiral as it is non-superimposable on its mirror image due to
its twisted nature (the twist comes from the structure of the double bonds needing to be at 90° angles to each other,
preventing the molecule from being planar).
3)
a) Just as hands are chiral a glove must also be chiral.
b) A nail has a plane of symmetry which goes down the middle making it a achiral.
c) A pair of sunglasses has a plane of symmetry which goes through the nose making it achiral.
d) Most written words are chiral. Look one in a mirror to confirm this.
4
a)

H OH H
HO *C * C
C C O
H
H HO H
b)

F F
F F
C * O
F C C
Cl H H

 Exercise 5.2.3
Circle all of the carbon stereocenters in the molecules below.
OH O
a) O OH b) c) H3 N
O O
O OH H3 N
O OH

mevalonate serine threonine

Answer

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 OH O
a) O OH b) c) H3 N
O O
O OH H3 N
O OH

mevalonate serine threonine

 Exercise 5.2.4
Circle all of the carbon stereocenters in the molecules below.
a)
OH
O
HO
O P O
OH O
2-methylerythritol-4-phopshate

O
b)
H N H
N CO2

S
biotin
c)
O
H
N
O
O N
H O
dihydroorotate

Answer
a)
OH
O
HO
O P O
OH O
2-methylerythritol-4-phopshate

O
b)
H N H
N CO2

S
biotin
c)
O
H
N
O
O N
H O
dihydroorotate

5.2.8 https://chem.libretexts.org/@go/page/31421
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!)
H OH HO H H CH3 H3C H
HO H HO H O O
H3N H3N
H H O H H O O O
glyceraldehyde alanine

HO H H OH
O O
H3C H3C
H NH3 H3N H
O O
lactate amphetamine

Here are some examples of molecules that are achiral (not chiral). Notice that none of these molecules has a stereocenter.
OH

OH
O HO CO2 HO

N CH3
OH OH CO2 CO2 H
dihydroxyacetone citrate pyridoxine
(vitamin B6)

O H H HO
O O
H3 C H3N
O HO NH3
O
pyruvate glycine dopamine
(amino acid) (neurotransmitter)

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.
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.
O 18O O

O P O 16O P R’O P OR’’’

O 17O O R’’O

phosphate labeled phosphate ester a chiral phosphate triester

(achiral) (chiral)

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.

5.2.9 https://chem.libretexts.org/@go/page/31421
 R''
R’’‘ N R’

N CH3 the rapid inversion of

CH3 amines makes them chiral

a chiral quaternary
ammonium R''' N R’
R''

 Exercise 5.2.5

Label the molecules below as chiral or achiral, and circle all stereocenters.
a) fumarate (a citric acid cycle intermediate)
O
O
O
O

b) malate (a citric acid cycle intermediate)

O
O
O
OH O

b) malate (a citric acid cycle intermediate)

O OH

Answer
a) achiral (no stereocenters)
O
O
O
O

b) chiral
O
O
O
OH O

c) chiral
O OH

 Exercise 5.2.6

Label the molecules below as chiral or achiral, and circle all stereocenters.
a) acetylsalicylic acid (aspirin)

5.2.10 https://chem.libretexts.org/@go/page/31421
 O OH

O O

b) acetaminophen (active ingredient in Tylenol)

H
N

O
HO

c) thalidomide (drug that caused birth defects in pregnant mothers in the 1960’s)
O

N O
NH
O O

Answer
a) achiral (no stereocenters)
O OH

O O

b) achiral (no stereocenters)

H
N

O
HO

c) chiral
O

N O
NH
O O

 Exercise 5.2.7

Draw both enantiomers of the following chiral amino acids.

O

HS OH

a) Cysteine NH2

N OH
b) Proline H

Answer

5.2.11 https://chem.libretexts.org/@go/page/31421
 O O

a) HS OH HS OH
NH2 NH2

O O
b)
N OH N OH
H H

 Exercise 5.2.8

Draw both enantiomers of the following compounds from the given names.
a) 2-bromobutane
b) 2,3-dimethyl-3-pentanol

Answer
Br Br
a)

HO HO
b)

 Exercise 5.2.9

Which of the following body parts are chiral?

a) Hands b) Eyes c) Feet d) Ears

Answer
a) Hands- chiral since the mirror images cannot be superimposed (think of the example in the beginning of the section)
b) Eyes- achiral since mirror images that are superimposable
c) Feet- chiral since the mirror images cannot be superimposed (Does your right foot fit in your left shoe?)
d) Ears- chiral since the mirror images cannot be superimposed

 Exercise 5.2.10

Circle the chiral centers in the following compounds.

a) b) c)
OH
HO
NH Br

Answer
a) b) c)
OH
HO
NH
Br

5.2.12 https://chem.libretexts.org/@go/page/31421
  Exercise 5.2.11

Identify the chiral centers in the following compounds.

a) H
H2 N CO2H
CH2CH2CO2-Na+

CH3
H3C
b)
CH3
O

c)

HO

Answer
H
a)
H2N CO2H
CH2CH2CO2-Na+

CH3
H3C
b)
CH3
O

c)

HO

5.2: The Reason for Handedness in Molecules - Chirality is shared under a CC BY-SA 4.0 license and was authored, remixed, and/or curated by
Jim Clark, Steven Farmer, Dietmar Kennepohl, Zachary Sharrett, Layne Morsch, Krista Cunningham, Tim Soderberg, William Reusch, &
William Reusch.
Current page by Dietmar Kennepohl, Jim Clark, Krista Cunningham, Layne Morsch, Steven Farmer, Tim Soderberg, William Reusch,
Zachary Sharrett is licensed CC BY-SA 4.0.
3.5: Naming chiral centers- the R and S system by Tim Soderberg is licensed CC BY-NC-SA 4.0. Original source:
https://digitalcommons.morris.umn.edu/chem_facpubs/1/.

5.2.13 https://chem.libretexts.org/@go/page/31421
5.3: 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]20
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.
Specific rotations are normally measured at 20°C, and this property may be indicated by the symbol [α]
20
D
. Sometimes the
solvent is specified in parentheses behind the specific rotation value, for example,
20 o
[α ] = +12 (chloroform)
D

For liquids, the specific rotation may be obtained using the neat liquid rather than a solution; in such cases the formula is
temp
[α ] (neat) = α × l × d
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 (Figure
5.3.1).

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

5.3.1 https://chem.libretexts.org/@go/page/31422
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.

6 8
4
2 7

1
Figure 5.3.1 : Operating principle of an optical polarimeter. 1. Light source 2. Unpolarized light 3. Linear polarizer 4. Linearly
polarized light 5. Sample tube containing molecules under study 6. Optical rotation due to molecules 7. Rotatable linear analyzer 8.
Detector. (CC BY-SA 3.0 Unported; Kaidor via Wikipedia)
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
lis 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 enantiomers have the following
specific rotations:
Carvone from caraway: [α ] 20
D
= +62.5
o
(this isomer may be referred to as (+)-carvone or d-carvone)
Carvone from spearmint: [α ] 20
D
= −62.5
o
(this isomer may be referred to as (–)-carvone or l-carvone)
and carvone enantiomers have the following specific rotations:

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 Lactic acid from muscle tissue: [α ] = +2.5 (this isomer may be referred to as (+)-lactic acid or d-lactic acid)
20
D
o

Lactic acid from sour milk: [α ] = −2.5 (this isomer may be referred to as (–)-lactic acid or l-lactic acid)
20
D
o

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).

CH CH=CHCH + HBr ⟶ (±)CH CH C HBrCH

3 3 3 2 3

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%.
 specific rotation of mixture 
% optical purity  = × 100%
 specific rotation of pure enantiomer 

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:
(% more abundant enantiomer  − 50) × 100%
ee =
50

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 %.

 Exercise 5.3.1

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.

5.3.3 https://chem.libretexts.org/@go/page/31422
 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

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, 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 of this technique is known as chiral resolution.

 Exercise 5.3.2

A 3.20 g sample of morphine ([α]D = -132) was dissolved in 10.0 mL of acetic acid ([α]D = 0). If it is put into a sample tube
with a path length of 2.00 cm, what would be its observed rotation (α)?

Answer
The specific rotation, [α]D = (observed rotation, α (degrees))/ [(pathlength, l (dm)) x (concentration, c (g/cm3))] = α/(l x c)
Solving for α, α = [α]D x l x c
([α]D = -132) x (l = 2.00 cm = 0.200 dm) x (c = 3.20 g / 10.0 cm3 = 0.320 g/cm3)
α = -132 x 0.200 dm x 0.320 g/cm3 = -8.45 o

 Exercise 5.3.3
Is the morphine in the previous excercise dextrorotatory or levorotatory?

Answer
Since morphine has a (-) rotation, it indicates that it rotates light to the left (counterclockwise) and morphine is levorotatory.

 Exercise 5.3.4

Label the following compounds as dextrorotatory or levorotatory.

a. sucrose ([α]D = + 66.7)
b. cholesterol ([α]D = - 31.5)
c. cocaine ([α]D = - 16)
d. chloroform ([α]D = 0)

Answer
a. sucrose ([α]D = + 66.7) dextrorotatory

5.3.4 https://chem.libretexts.org/@go/page/31422
 b. cholesterol ([α]D = - 31.5) levorotatory
c. cocaine ([α]D = - 16) levorotatory
d. chloroform ([α]D = 0) neither, not optically active

 Exercise 5.3.5a

The specific rotation of (S)-carvone is (+) 61o when measured neat (pure liquid sample with no solvent). The optical rotation of
a neat sample of a mixture of R and S carvone is measured at (-) 23 o.
a) Which enantiomer is in excess?

Answer
Since the pure S enantiomer ((+) 61o) is dextrorotatory (positive, clockwise), the R enantiomer must be levorotatory. The
observed rotation of the mixture is levorotatory since its negative (counterclockwise). This means the mixture must contain
more of the R enantiomer than the S enantiomer.

 Exercise 5.3.5b

b) What are the percentages of (S)- and (R)- carvone in the sample mixture?

Answer
Optical rotation (α) of the (R/S mixture) = [fraction (S) x [α]D (S)] + [fraction (R) x [α]D (R)]
To determine the fraction of S and R, we make y = fraction (S) and 1 – y = fraction (R)
-23o = y x (61o) + (1 – y) x (-61o) solving for y: y = 0.3114 and (1-y) = 0.6885
Therefore the percentage of (S)-carvone is 31.1 % and (R)-carvone is 68.9 %

 Exercise 5.3.5c

c) What is the ee (enantiomeric excess)?

Answer
ee = [(% more abundant isomer – 50) x 100]/50 = [(68.9 – 50) x100]/50 = 37.8 % ee

 Exercise 5.3.6a

Determine the ee’s of the following from the percentages

95 % (R)- tartaric acid and 5.0 % (S)- tartaric acid

Answer
[(95 – 50) x 100] / 50 = 90 % ee (R)-tartaric acid

 Exercise 5.3.6b

Determine the ee’s of the following from the percentages

75 % (S)- limonene and 25 % (R)- limonene

Answer
[(75 – 50) x 100] / 50 = 50 % ee (S)- limonene

5.3.5 https://chem.libretexts.org/@go/page/31422
  Exercise 5.3.6c

Determine the ee’s of the following from the percentages

85 % (R) cysteine

Answer
(85 – 50) x 100] / 50 = 70 % ee (R)-cysteine

 Exercise 5.3.6d

Determine the ee’s of the following from the percentages

50 % (S) alanine

Answer
(50 – 50) x 100] / 50 = 0 % ee, racemic mixture

5.3: Optical Activity is shared under a CC BY-SA 4.0 license and was authored, remixed, and/or curated by Steven Farmer, Dietmar Kennepohl,
Zachary Sharrett, Krista Cunningham, Tim Soderberg, & Tim Soderberg.

5.3.6 https://chem.libretexts.org/@go/page/31422
5.4: 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.

CO2 Na
H *C OH
HO *C H
CO2 NH4
sodium ammonium tartrate

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 below. 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.

5.4: Pasteur's Discovery of Enantiomers is shared under a CC BY-SA 4.0 license and was authored, remixed, and/or curated by Steven Farmer,
Dietmar Kennepohl, Krista Cunningham, William Reusch, & William Reusch.

5.4.1 https://chem.libretexts.org/@go/page/31423
5.5: 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).
The Cahn-Ingold-Prelog rules of assign priorities the groups directly bonded to the chiral carbon. Having ranked the four groups
attached to a chiral carbon, we describe the stereochemical configuration around the carbon by orienting the molecule so that the
group with the lowest ranking (4) is given a dash bond to indicate it points directly away from us. We then look at the three
remaining substituents, which now appear to radiate toward us which is shown by using wedge bonds. If a curved arrow drawn
from the highest to second-highest to third-highest ranked substituent is clockwise, we say that the chirality center has the (R)
configuration (Latin rectus, meaning “right”). If an arrow from is counterclockwise, the chirality center has the (S) configuration
(Latin sinister, meaning “left”). To remember these assignments, think of a car’s steering wheel when making a Right (clockwise)
turn. Note, the (R) or (S) configurations represent the two enantiomers of a chiral molecule. The (R) or (S) configuration is often

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added as a prefix, in parenthesis, to a chiral molecule's name to indicate which enantiomer is being discussed (e.g., (R)-2-
bromobutane). If more than chiral carbon is present in a chiral molecule, each carbon's number is included before the (R) or (S)
configuration. Ex: (2R,4S,6R)-2-bromo-6-chloro-4-methylheptane.
mirror

4 4

1
C C 1
3 3
2 2

Reorient to place Reorient to place

the lowest priority the lowest priority
substituent (4) substituent (4)
going away. going away.

4 4
1 2 2 1
C C

3 3

(R ) configuration (S ) configuration
(clockwise) (counterclockwise)

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 atom with a higher atomic number takes
precedence over a atom with a lower atomic number. Hydrogen is the lowest possible priority atom, because it has the lowest
atomic number.
1. The atom with higher atomic number has higher priority (I > Br > Cl > S > P > F > O > N > C > H).
2. When comparing isotopes, the atom with the higher mass number has higher priority [18O > 16O or 15N > 14N or 13C > 12C or T
(3H) > D (2H) > H].

Rule 2
If there are two or more substituents which have the same element directly attached to chiral carbon, proceed along the substituent
chains until a point of difference is found. 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.
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 two hydrogen atoms and a 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.
lower
higher
H H H
H C vs. H C C
H H H

The "-H" (left) ranks lower than the "C-" (right) based on the relative molecular weights at the first point of difference.

 Example 5.5.1

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 H H H H H
C C H C O H C O H C Br
H H H H H
lower higher lower higher

H H H H H H H H
C C Br C O H C C H C C C H
H H H H H H H H
lower higher lower higher

 Worked Exercise 5.5.1

For the following pairs of substituents, determine which would have the higher and lower priority based on the Cahn-Ingold-
Prelog rules. Explain your answer.
H CH3 CH3 Br
C CH3 C CH3 C CH3 C CH3
H H H H

H CH3 CH2CH3 CH2CH3

C CH2 Cl C CH3 C CH2 OH C CH2 O CH3
H H H H

Answer
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-methylethyl ranks higher in priority than ethyl, as shown below:
lower higher

H CH3
C CH3 C CH3
H H

equal

The "C-" (right) ranks higher than the "H-" (left) based on
the first point of difference and their relative atomic numbers.
However:
lower higher

CH3 Br
C CH3 C CH3
H H

equal

In this case, even though the bold carbon on the right structure has two
connections to a non-hydrogen atom (C), it is the lower priority.
This is because one of the atoms attached to the bold carbon on the left molecule

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 ranks higher than any of the atoms attached to the bold carbon on the right structure,
since Br has a higher atomic number than C.
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.
first point of difference

lower higher

H CH3
C CH2 Cl C CH3
H H

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.
lower higher
CH2CH3 CH2CH3
C CH2 O H C CH2 O CH3
H H

first point of difference

Rule 3
For assigning priority, multiple bonds are treated as if each bond of the multiple bond is bonded to a unique atom. For example, an
alkene substituent (CH2=CH-) has higher priority than an ethyl substituent (CH3CH2-). The alkene carbon priority is "two" bonds
to carbon atoms and one bond to a hydrogen atom compared with the ethyl carbon that has only one bond to a carbon atom and two
bonds to two hydrogen atoms. Similarly, alkyne substituent (HCC-) would have an even higher priority because the alkyne carbon
is treated as if it is bonded to three carbons. This method remains the same with compounds containing a carbonyl (C=O) group.
The carbon of an aldehyde substituent (O=CH-) is treated as if it is bonded to a hydrogen and two oxygen atoms.
H H C C
C C is prioritized as H C C H
H H
alkene

C C
C C H is prioritized as C C H

alkyne
C C

H O C
C O is prioritized as H C O
C
aldehyde

Determining (R) or (S) Configuration Using a Molecular Model

In order to demonstrate how to determine the (R)/(S) configuration of the chiral carbon in the following molecule using molecular
models, first construct a model of the bromoethanol structure:
H3C
Br
C H
HO

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First make a molecular model of a tetrahedral carbon with four different substituents. In many cases, this will appear as a carbon
with four bonds with a different colored ball attached to each bond.
For the molecule in question, determine the location of the chiral carbon and assign CIP priorities to the substituents. In this case,
Br gets the highest priority because it has the highest atomic number. The O in the OH substituent gets priority 2 and the C in CH3
gets priority 3. Lastly, H gets the lowest priority, 4, because it has the smallest atomic number.
3
H3C 1
Br
C
H
HO 4
2

Now take your molecular model and orientate it to match the molecule in question. Remember in the dash/wedge representation,
two regular bonds are in the plane of the page. The wedge bond is coming toward you and the dashed bond is going away from
you. If you were to hold a piece of paper directly in front of you, the substituents with the regular bond should both be touching the
piece of paper. The dashed bond should be pointing behind the piece of paper and the wedge bond should be pointing in front.
Br

H3 C
H 3C
C Br
C H
HO
HO

In this structure, the bromine is going away from you, the hydrogen is coming toward you and the hydroxide and methyl
groups are in the plane of the page.
Then based on the position, assign each substituent on the chiral carbon a colored ball on your molecular model. In this case,
bromine is going away so it is assigned the green ball. The hydrogen is coming toward you so it is assigned the blue ball. The last
two substituents are in the plane of the page, however, the CH3 is positioned higher so it is assigned the red ball which leaves OH
being assigned the black ball.
Lastly, grab onto the ball for the lowest priority substitutent, in this case the blue one, and point the other three substituents towards
you. The three bonds should be angled towards you as if they all have wedge bonds. Assign the original substituents and their
corresponding CIP priorities to the three colored balls. The green ball was assigned to bromine which was given priority one. The
OH was assigned to the black ball and given priority two. The CH3 was assigned to the red ball and given priority three. In this
case the priorities are going counter clockwise so the chiral carbon has an (S) configuration.

CH3 3
= =
Br OH 1 2
(S )-configuration

Determining (R) or (S) Configuration Without a Molecular Model

If a molecular model cannot be used there are a couple of simple methods which can be applied if the dash/wedge bond system is
being used.
After assigning CIP priorities, if the lowest priority substituent (4) is on the dash bond the configuration of substituents 1-3 can be
assigned directly. As shown in the figure below, the configuration of substituents 1-3 does not change when moving to sight down
the bond of substituent 4. In both cases, substituents 1-3 are ordered in a counterclockwise fashion which gives the chiral carbon an
(S) configuration.
1 4
4 1 3
C = C
3
2 2

counterclockwise counterclockwise
(S )-configuration (S )-configuration

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The opposite is true if the lowest priority substituent (4) is on the wedge bond. As shown in the figure below, the configuration of
substituents 1-3 is inverted when moving to sight down the bond of substituent 4. When the lowest priority substituent is on the
wedge bond, the configuration of substituents 1-3 can be assigned directly only if the direction is inverted. i.e. clockwise = (S) and
counterclockwise = (R).

1 4
3 1 2
C = C
4
2 3

counterclockwise clockwise
(R)-configuration

With the lowest priority group in front, drawing an arc from 1 to 2 to 3 gives the reverse of the configuration.
However, if the lowest priority substituent is on one of the regular bonds when the dash/wedge system is being used then
configurations are best assigned by changing perspectives. This method can also be used if the three-dimensional configuration of
the chiral carbon is represented. First, locate the chiral carbon and assign CIP priorities to its substituents. Then while perceiving
the drawn molecule as a three-dimensional image, mentally change your perspective such that you are looking down the bond
between the chiral carbon and the lowest CIP ranked substituent (#4). If done correctly, the bonds for substituents 1-3 should be
coming towards you as wedge bonds. You can then follow the direction of the CIP priority numbers to determine the (R)/(S)
configuration of the chiral carbon.
O O
C C 1
H CH2 = H CH2
3
C CH * C CH
H 3 4 H 3
H2C CH3 H2C CH3
2

Locate the chiral carbon and assign CIP priorities to its substituents.
O
H O
C C
H CH2 = H
H 3C CH2
C CH C
H 3
H2C CH3 CH2
H 3C

Mentally sight down the bond between the chiral carbon and the lowest CIP ranked substituent.
This bond is shown in magenta.
H O
C
3 H
H3 C CH2
C 1
CH2
H3 C 2

clockwise
(R)-configuration
Follow the direction of the CIP priority numbers to determine the (R)/(S) configuration.

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Drawing the Structure of a Chiral Molecule from its Name
Draw the structure of (S)-2-Bromobutane:
1) Draw the basic structure of the molecule and determine the location of the chiral carbon.
H
H3CH2C *C CH3
Br

2) Determine the chiral carbon's substituents and assign them a CIP priority.
-H (Priority 4)
-CH3 (Priority 3)
-CH2CH3 (Priority 2)
-Br (Priority 1)
3) Draw the chiral carbon in a dash/wedge form and add the lowest priority substituent to the dash bond. In this case, the lowest
priority substituent is -H.

*C H

4) Add the remaining substituents in a clockwise fashion for (R) and a counterclockwise fashion for (S).
1 1
*C H *C H
2 3
3 2

clockwise counterclockwise
(R)-configuration (S )-configuration

The molecule posed in this question has an (S) configuration so the remaining substituents are added in a counterclockwise fashion.
1 Br
*C H *C H
3 CH3
2 H3CH2C
counterclockwise
(S )-2-bromobutane
(S )-configuration

 Exercise 5.5.1
1) Orient the following so that the least priority (4) atom is paced behind, then assign stereochemistry ((R) or (S)).

2) Draw (R)-2-bromobutan-2-ol.
3) Assign (R)/(S) to the following molecule.

4) Which in the following pairs would have a higher CIP priority?

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 a. -H or -Cl
b. -Br or -I
c. -CH2OH or -OCH3
d. -CH2CH3 or -CH=CH2
e. -NH2 or -OH
5) Rank the following substituents in order of their CIP priority:
a. -H, -OCH3, -CH2OH, -OH
b. -OH, -CO2H, -CH=O, -CH2OH
c. -CN, -NH2, -CH=O, -NHCH3
d. -SH, -SCH3, -OH, -OOCH3
6) Determine if the chiral carbon in the following molecules have an (R) or (S) configuration. Red = Oxygen & Blue =
Nitrogen.
a)

GLmol
b)

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 GLmol
Answer
1) A is (S) and B is (R).

2)

3) The stereocenter is (R).

4)
a. -Cl
b. -I
c. -OCH3
d. -CH=CH2
e. -OH
5) Rank the following substituents in order of their CIP priority:
a. -OCH3, -OH, -CH2OH, -H,
b. -OH, -CO2H, -CH=O, -CH2OH
c. -NHCH3, -NH2, -CH=O, -CN
d. -SCH3, -SH, -OOCH3, -OH
6)
a) The chiral carbon is (R). The four substituents of the chiral carbon are -OH (1), -NH2 (2), -CH3 (3), and -H (4). Then
looking down the lowest priority bond, you should roughly see what appears in the picture below. The substituents with
priorities 1-3 are ordered in a clockwise fashion so the chiral carbon is (R).

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 b) The chiral carbon is (S). The four substituents of the chiral carbon are -CO2H (1), -OH (2), -CH2CH2CH3 (3), and -H (4).
Then looking down the lowest priority bond, you should roughly see what appears in the picture below. The substituents
with priorities 1-3 are ordered in a counterclockwise fashion so the chiral carbon is (S).

 Exercise 5.5.2

Identify which substituent in the following sets has a higher ranking.

a. -H or -CH3
b. -CH2CH2CH3 or CH2CH3
c. -CH2Cl or CH2OH

Answer
a. -CH3
b. -CH2CH2CH3
c. -CH2Cl

 Exercise 5.5.3

Identify which substituent in the following sets has a higher ranking.

a. -NH2 or -N=NH
b. -CH2CH2OH or -CH2OH
c. -CH=CH2 or -CH2CH3

Answer
a) -N=NH
b) -CH2OH
c) -CH=CH2

 Exercise 5.5.4

Place the following sets of substituents in each group in order of lowest priority (1st) to highest priority (4th)
a. -NH2, -F, -Br, -CH3
b. -SH, -NH2, -F, -H

Answer
a) -CH3 < -NH2 < -F, < -Br
b) -H < -NH2 < -F, < -SH

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 Exercise 5.5.5

Place the following sets of substituents in each group in order of lowest priority (1st) to highest priority (4th)
a. -CH2CH3, -CN, -CH2CH2OH, -CH2CH2CH2OH
b. -CH2NH2, -CH2SH, -C(CH3)3, -CN

Answer
a) -CH2CH3 < -CH2CH2OH < -CH2CH2CH2OH, < -CN
b) -C(CH3)3 < -CH2NH2 < -CN < -CH2SH

 Exercise 5.5.6

Assign the following chiral centers as (R) or (S).

a) Br H b) H Br c) SHH

F I Cl CH3 H CH3

Answer
a) (S): I > Br > F > H. The lowest priority substituent is going backwards so following the highest priority, it goes left
(counterclockwise).
b) (R): Br > Cl > CH3 > H. Using a model kit, you need to rotate the H to the back position where the Br is. This causes the
priority to go to the left (clockwise) when looking at it with the H in the back position. Alternatively, if you do not have a
model kit, you can imagine the structure 3-dimensionally and since the lowest priority (H) is facing up (as drawn), if you
look at it from below, starting with Br (1st priority) and moving towards Cl (2nd priority), you are moving right (clockwise)
which represents (R) stereochemistry.
c) Neither (R) or (S): Since there are two identical substituents (H’s) the molecule is achiral and cannot be assigned (R) or
(S).

 Exercise 5.5.7

Assign the following chiral centers as (R) or (S).

CH
a) CNCH NH b) c) OHCH
2 2 C COOH 3
C C
H OH C H 2N Br
HOH2C H

Answer
a) (R): OH > CN (C triple bonded to N) > CH2NH2 > H. The H needs to be moved to the back position which causes the
priority to go to the right (clockwise) which indicates (R).
b) (S): COOH > CH2OH > C CH > H. Since the H is coming forward, you can assign the priority and it goes to the right
(clockwise which would be (R)) but since the lowest priority is forward, you have to switch it to (S). Alternatively, you can
rotate the molecule to put the lowest priority to the back and you’ll see that it rotates left (or counterclockwise) for (S).
c) (S): Br > OH > NH2 > CH3. Since the lowest priority is going back, you can follow the priority and see that it is going
left (counterclockwise) and therefore (S).

 Exercise 5.5.8

Draw the structure of (R)-2-bromohexane.

Answer

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 Br H

 Exercise 5.5.9

Draw the structure of (S)-2-methyl-3-pentanol.

Answer

H OH

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.

5.5: Sequence Rules for Specifying Configuration is shared under a CC BY-SA 4.0 license and was authored, remixed, and/or curated by Steven
Farmer, Ekta Patel, Ifemayowa Aworanti, Dietmar Kennepohl, Zachary Sharrett, Layne Morsch, Krista Cunningham, & Krista Cunningham.

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5.6: 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 two molecules which are stereoisomers (same molecular formula, same connectivity, different arrangement of
atoms in space) but are not enantiomers. Unlike enantiomers which are mirror images of each other and non-superimposable,
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. In order for diastereomer stereoisomers
to occur, a compound must have two or more stereocenters.

Introduction
So far, we have been analyzing compounds with a single chiral center. Next, we turn our attention to those which have multiple
chiral centers. We'll start with some stereoisomeric four-carbon sugars with two chiral centers.
chiral center #1
O OH
OH
H
OH
chiral center #2

We will start with a common four-carbon sugar called D-erythrose.

H OH O
C2: (R )
HO 4 2
3 1
H C3: (R )
HO H
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).

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 enantiomers

H OH O O HO H
HO (R ) (S ) OH
(R ) H H (S )

HO H H OH
D-erythrose L-erythrose

Notice that both chiral centers in L-erythrose both have the (S) configuration. To avoid confusion, we will simply refer to the
different stereoisomers by capital letters.
Now let's consider all the possible stereoisomers.
Look first at compound A below. Both chiral centers in have the (R) configuration (you should confirm this for yourself!). The
mirror image of Compound A is compound B, which has the (S) configuration at both chiral centers. If we were to pick up
compound A, flip it over and put it next to compound B, we would see that they are not superimposable (again, confirm this for
yourself with your models!). A and B are nonsuperimposable mirror images: in other words, enantiomers.
mirror plane

O HO H H OH O
enantiomers
(R ) OH HO (S )
H (R ) (S ) H diastereomers
H OH HO H
A B

O HO H H OH O
(S ) OH HO (R )
H (R ) (S ) H
HO H H OH
C D

Now, look at compound C, in which the configuration is (S) at chiral center 1 and (R) at chiral center 2. Compounds A and C are
stereoisomers: they have the same molecular formula and the same bond connectivity, but a different arrangement of atoms in
space (recall that this is the definition of the term 'stereoisomer). However, they are not mirror images of each other (confirm this
with your models!), and so they are not enantiomers. By definition, they are diastereomers of each other.
Notice that compounds C and B also have a diastereomeric relationship, by the same definition.
So, compounds A and B are a pair of enantiomers, and compound C is a diastereomer of both of them. Does compound C have its
own enantiomer? Compound D is the mirror image of compound C, and the two are not superimposable. Therefore, C and D are a
pair of enantiomers. Compound D is also a diastereomer of compounds A and B.
This can also seem very confusing at first, but there some simple shortcuts to analyzing stereoisomers:

Stereoisomer Shortcuts
If all of the chiral centers are of opposite (R)/(S) configuration between two stereoisomers, they are enantiomers.
If at least one, but not all of the chiral centers are opposite between two stereoisomers, they are diastereomers.

These shortcuts to not take into account the possibility of additional stereoisomers due to alkene groups: we will come to that
later

Here's another way of looking at the four stereoisomers, where one chiral center is associated with red and the other blue. Pairs of
enantiomers are stacked together.

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 chiral center #1
O OH
possible configurations:
OH (R ,R ) (R ,S )
H
(S ,S ) (S ,R )
OH
chiral center #2

We know, using the shortcut above, that the enantiomer of (R,R) must be (S,S) - both chiral centers are different. We also know that
(R,S) and (S,R) are diastereomers of (R,R), because in each case one - but not both - chiral centers are different.

Determining the Maximum Number of Stereoisomers for a Compound

In general, a structure with n stereocenters will have a maximum of 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).
enantiomers

OH OH O OH OH O
HO (R ) (R ) HO (S ) (S )
(R ) (S ) H (S ) (R ) H
OH OH OH OH
D-glucose L-glucose

diastereomers
OH OH O diastereomers
HO (S ) (R )
(R ) (S ) H
OH OH

D-galactose

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
OH OH O
HO (R ) (S ) L-galactose
(S ) (R ) H
OH OH

OH OH O
HO (R ) (S ) L-mannose
(R ) (S ) H (epimer of D-glucose)
OH OH

OH OH O
HO (S ) (R ) L-gulose
(R ) (R ) H (diasteromer of D-glucose)
OH OH

5.6.3 https://chem.libretexts.org/@go/page/31425
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.
O
H 3C CH3
CH3
H3C
OH OH
H3C H3C
O OH

O OH
CH3

erythronolide B

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.

 Exercise 5.6.1

Determine the number of stereoisomers a molecule can have with…

a. 3 chiral centers
b. 1 chiral center
c. 6 chiral centers

Answer
Since a molecule with n chiral centers can have 2n stereoisomers…
a. 23 = 8 possible stereoisomers
b. 21 = 2 possible stereoisomers
c. 26 = 64 possible stereoisomers

 Exercise 5.6.2a

What is the relationship between enantiomers?

Answer
They are mirror images of each other and when 2 or more chiral centers are present, every stereocenter is the opposite in its
enantiomer.

 Exercise 5.6.2b
How does the stereochemistry in diastereomers differ from each other?

Answer
In diastereomers, one or more of the chiral centers is the opposite but they all can’t be the opposite or else they’d be
enantiomers.

5.6.4 https://chem.libretexts.org/@go/page/31425
 Exercise 5.6.2c

What are epimers?

Answer
Epimers are when only one chiral center is the opposite (in molecules with 2 or more chiral centers) in its diastereomer.

 Exercise 5.6.3a

Draw the structure of (2R,3R) 2-fluoro-3-methylhexane.

Answer
H
F
H
2R,3R

 Exercise 5.6.3b

Draw both diastereomers of (2R,3R) 2-fluoro-3-methylhexane.

Answer
H
H
F H
H F
2R,3S 2S,3R

 Exercise 5.6.3c

Draw the enantiomer of (2R,3R) 2-fluoro-3-methylhexane.

Answer

H
H
F
2S,3S

 Exercise 5.6.4a

Draw the structure of L-galactose, the enantiomer of D-galactose.

OH OH O
HO
H
OH OH

S, R, R, S
D-galactose

Answer

5.6.5 https://chem.libretexts.org/@go/page/31425
 OH OH O
HO
H
OH OH

S, R, R, S
L-galactose

 Exercise 5.6.4b

Draw a diastereomer of D-galactose that is an epimer.

Answer
You can draw an epimer by drawing D-galactose with 1 (and only 1) of its chiral centers reversed. Here’s an example when
you switch only the first chiral center (in red). (There are 3 other epimers that could be drawn as long as you only swap a
single chiral center in the diastereomer that you use.)
OH OH O
HO
H
OH OH

R, R, R, S

 Exercise 5.6.4c

Identify if the following diastereomer of galactose is an epimer of D- galactose or L- galactose.

OH OH O
HO
H
OH OH

Answer
OH OH O
HO
H
OH OH

S, R, S, S

Since the diastereomer above only varies from L-galactose by 1 chiral center, the above is an epimer in relationship to L-
galactose. Since it varies from D-galactose by 3 chiral centers, it is not an epimer but a diastereomer. Since not all of the
chiral centers are swapped, it is not an enantiomer!

 Exercise 5.6.5a
For the compound shown below, label each chiral center as R or S.
OH

Answer
S OH

R F
S

5.6.6 https://chem.libretexts.org/@go/page/31425
  Exercise 5.6.5b
How many stereoisomers are possible for the compound in part a)?

Answer
Since there are 3 chiral centers, 23 = 8 possible stereoisomers.

 Exercise 5.6.6

Consider the stereoisomers below.

OH OH OH OH

i ii iii iv

a. Which is/are an enantiomer of i?

b. Which is/are a diastereomer of ii?
c. Which is/are an epimer of i?

Answer
a. iv is an enantiomer of i since both chiral centers are switched and they are non superimposable mirror images.
b. i & iv are diastereomers of ii since they are stereoisomers that are not mirror images.
c. ii and iii are epimers of i since they are diastereomers with only 1 chiral center switched and the other one the same.

 Exercise 5.6.7

Consider the 8 stereoisomers below.

OH OH OH
OH

OH OH OH
OH
i ii iii iv

OH OH OH
OH

OH OH OH
OH
v vi vii viii

a. Which is/are an enantiomer of i?

b. Which is/are a diastereomer of i?
c. Which is/are an epimer of i?

Answer
a. v is an enantiomer since all three chiral centers are switched and they are non superimposable mirror images.
b. ii, iii, iv, vi, vii & viii are diastereomers of i since they are stereoisomers that are not mirror images.
c. ii,iii & viii are epimers of i since they are diastereomers with only 1 chiral center switched and the other chiral centers
the same.

5.6: Diastereomers is shared under a CC BY-SA 4.0 license and was authored, remixed, and/or curated by Steven Farmer, Dietmar Kennepohl,
Zachary Sharrett, Tim Soderberg, & Tim Soderberg.

5.6.7 https://chem.libretexts.org/@go/page/31425
5.7: 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.

Introduction
A meso compound is an achiral compound that has chiral centers. A meso compound contains an internal plane of symmetry which
makes it superimposable on its mirror image and is optically inactive although it contains two or more stereocenters. Remember,
an internal plane of symmetry was shown to make a molecule achiral in Section 5.2.
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 reflected
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, resulting the
molecule being optically inactive.

Identification
A meso compound must have:
1. Two or more stereocenters.
2. An internal plane of symmetry, or internal mirror, that lies in the compound.
3. Stereochemistry that cancels out. This means reflected stereocenter should have the same substituents and be inverted. For
instance, in a meso compound with two stereocenters one should be R and the other S.
The compounds 2,3-dichlorobutane contains two chiral carbons and therefore would be expected to provide 22 = 4 different
stereoisomers. These stereoisomers should be made up of two pairs of enantiomers.
Cl Cl
H3C *C C* CH3
H H

2,3-dichlorobutane

After drawing out all the possible stereoisomers of 2,3-dichlorobutane, the pair on the right in the figure below are mirror images.
Also, they are non-superimposable because they have distinctly different conformation (R,R & S,S). This makes the pair

5.7.1 https://chem.libretexts.org/@go/page/31426
enantiomers of each other. However, the pair on the left represent a meso compound, they both are identical despite being mirror
images.
mirror mirror

H H (R ) Cl Cl (S )
H3C (S ) Cl Cl CH3 H3C (R ) H H C CH3
C C C
C C C C
H3C (R ) HCl Cl
H (S ) CH3 H3C (R ) HCl Cl
H (S ) CH3

identical enantiomers
(meso)

Upon further investigation, the meso compound has an internal plane of symmetry which is not present in the pair of enantiomers.
The plane of symmetry in the meso compound comes about because there are two chiral carbons present, both chiral carbons are
identically substituted (Cl, H, CH3), and one chiral carbon is R and the other is S. Despite being represented as mirror images, both
structures represent the same compound. This is best proven by making molecular models of both representations and then
superimposing them. Overall, 2,3-dichlorobutane only has three possible stereosiomers, the pair of enantiomers and the meso
compound.
H H
H 3C CH3
(S ) C Cl Cl C (R ) internal plane of
symmetry
(R ) C Cl C (S )
H 3C Cl CH3
H H

identical
(meso)

When looking for an internal plane of symmetry, it is important to remember that sigma bonds (single bonds) can rotate. Just
because the immediate representation of a molecule does not have a plane of symmetry does not mean that one cannot be obtained
through rotation. Often the substituents attached to a stereocenter need to be rotated to recognize the internal plane of symmetry. As
the stereocenter is rotated, its configuration does not change. Building a molecular model when considering a possible meso
compound is an invaluable tool because it allows for easy rotation of chiral carbons. An example of how rotation of a chiral carbon
can reveal an internal plane of symmetry is shown below.
rotated

CH3 H
Cl H3C
C H C Cl internal plane of
symmetry
C Cl C Cl
H 3C H H3C H
meso
compound

 Example 5.7.1

Below are the two mirror images of (meso)-2,3-Butanediol. Because it is a meso compound, the two structures are identical.
Show that both mirror images can be obtained by simply rotating the three-dimensional structure provided below.
mirror

OH HO CH3
H 3C
H H
H H
CH3 H 3C
HO OH

(meso)-2,3-butanediol

5.7.2 https://chem.libretexts.org/@go/page/31426
 GLmol
 Example 5.7.2
CO2H
HO H
C chiral center

C chiral center
HO H
CO2H
1

1 has a plane of symmetry (the horizontal plane going through the red broken line) and, therefore, is achiral; 1 has chiral
centers. Thus, 1 is a meso compound.

 Example 5.7.3

chiral center chiral center

H3 C CH3

This molecules has a plane of symmetry (the vertical plane going through the red broken line perpendicular to the plane of the
ring) and, therefore, is achiral, but has has two chiral centers. Thus, its is a meso compound.

Other Examples of Meso Compounds

Meso compounds can exist in many different forms such as pentane, butane, heptane, and even cycloalkanes. Although two chiral
carbons must be present, meso compounds can have many more. Notice that in every case a plane of symmetry is present.
OH OH
F H F H CH3
H Cl H Cl I
H F H F
H F H F
Cl H F H F H H3C I
OH OH

In general, a disubstituted cycloalkane is meso if the two substituents are the same and they are in a cis conformation. Trans
disubstituted cycloalkanes are not meso regardless if the two substituents are the same.

5.7.3 https://chem.libretexts.org/@go/page/31426
 ≡ not meso

trans -1,3-dimethylcyclohexane

1,3-dimethylcyclohexane
≡ meso

cis -1,3-dimethylcyclohexane

Optical Activity Analysis of a Meso Compound

When the optical activity of a meso compound is attempted to be determined with a polarimeter, the indicator will not show (+) or
(-). It simply means there is no certain direction of rotation of the polarized light, neither levorotatory (-) and dexorotatory (+)
because a meso compound is achiral (optically inactive). Investigations of isomeric tartaric acid (2,3-dihydroxybutanedioic acid),
carried out by Louis Pasteur in the mid 19th century, were instrumental in elucidating some of the subtleties of stereochemistry.
Tartaric acid, has two chiral but only three stereoisomers. Two of these stereoisomers are enantiomers and the third is an achiral a
meso compound. Some physical properties of these stereoisomers of tartaric acid are given in the table below. Notice that the
enantiomers have the same amount of optical rotation but in different directons. Meso-tartaric acid produces no optical rotation
because it is achiral and not optically active. Meso-tartaric acid is actually a diastereomer of both (-) and (+)-tartaric acid, which
gives it a distinctly different melting point.
mirror
O O O
OH HO H
C C C
HO C H H C OH HO C OH internal plane of
symmetry
HO C OH HO C OH HO C OH
C C C
H H H
O O O

(−)-tartaric acid (+)-tartaric acid (meso )-tartaric acid

(+)-tartaric acid: [α]D = +13º m.p. 172 ºC

(–)-tartaric acid: [α]D = –13º m.p. 172 ºC

meso-tartaric acid: [α]D = 0º m.p. 140 ºC

 Exercise 5.7.1

1) Determine which of the following molecules are meso.

a) b) c) OH
Cl CH2CH3
HO Cl
CH2CH3

CH3
d) Br e) f)
H3CH2C H
C
C
Br H3CH2C CH3
H

2) Explain why 2,3-dibromobutane has the possibility of being a meso compound while 2,3-dibromopentane does not.
3) Observe the following compound and determine if it is a meso compound. If so indicate the plane of symmetry. Red =
oxygen. Remember sigma bonds are able to rotate.

5.7.4 https://chem.libretexts.org/@go/page/31426
 GLmol
Answer
1) A C, D, E are meso compounds.
2) One of the requirements of a meso compound is that the reflected chiral carbons have the same substituents. The
compound 2,3-dibromobutane, fulfills this requirement (Br, H, CH3) and can possibly be a meso compound if the two
chiral carbons have the appropriate configuration (R & S). The substituents of the two chiral carbons in 2,3-
dibromopentane do not have the same substituents (Br, H, CH3 vs. Br, H, CH2CH3). This 2,3-dibromopentane cannot form
a meso compound regardless of the configurations of its chiral carbons.
Possible plane
of symmetry

Br Br Br Br
H3C C* C* CH3 H3C C* C* CH2CH3
H H H H
2,3-Dibromobutane 2,3-Dibromopentane

3) The compound is meso.

Plane of Symmetry

H3 C CH3

OH

Exercise 5.7.1
Which of the following are meso compounds?

5.7.5 https://chem.libretexts.org/@go/page/31426
 a) H H b) H H c) H OH
HO OH HO Cl HO Cl
Cl Cl Cl OH Cl H

Answer
a) This is a meso compound. There is an internal plane of symmetry (dashed line shown in red) between the C’s (and it has
stereochemistry of S & R).

H H
HO OH
Cl Cl

b) This is not a meso compound. No matter how you rotate the C-C bond, you do not see a plane of symmetry (and its
stereochemistry is S & S)
c) This is a meso compound. There is an internal plane of symmetry (dashed line shown in red) that can be seen when you
rotate the C-C bond (and it has stereochemistry of S & R).

H OH H H
HO Cl HO OH
Cl H Cl Cl

 Exercise 5.7.2

Which of the following are meso compounds?

a) Br Br b) Br Br c) Br

Br

Answer
a) This is not a meso compound. There is no plane of symmetry and has stereochemistry of S & S.
Br Br
S S

b) This is a meso compound. There is an internal plane of symmetry (dashed line shown in red) and it has stereochemistry
of R & S.

Br Br
R S

c) This is not a meso compound (even though it has planes of symmetry). The plane of symmetry shown in red makes it so
that both chiral centers have symmetrical groups (the ring) and thus the compound is not chiral (so it can’t be a meso
compound).

Br

Br

5.7.6 https://chem.libretexts.org/@go/page/31426
  Exercise 5.7.3
Which of the following are meso compounds?

a) OH b) c)
Cl CH2CH3
HO Cl
CH2CH3

Answer
a) This is a meso compound. If you rotate between the C-C bond, you can see that it has a mirror plane between the C’s
(shown in red on the structure to the right). Notice how rotating a C-C bond doesn’t change the stereochemistry of the
molecule (S & R).
OH OH
S S
Cl CH2CH3 Cl CH2CH3
HO Cl Cl CH2CH3
R R
CH2CH3 OH

b) This is a meso compound. You can see the plane of symmetry in red and the compound has stereochemistry of S & R.

S R

c) This is not a meso compound. There is no plane of symmetry and it has stereochemistry of S & S.

S S

 Exercise 5.7.4
Determine (and draw) if any of the forms of 3,4-dichlorohexane are a meso compound.

Answer
Looking at the 4 different possibilities below, i & ii are equivalent structures (with R & S stereochemistry) so it is a meso
compound. iii & iv are not meso compounds but are enantiomers to each other.
Cl Cl Cl Cl
=
R S S R R R S S
Cl Cl Cl Cl

i ii iii iv

5.7: Meso Compounds is shared under a CC BY-SA 4.0 license and was authored, remixed, and/or curated by Steven Farmer, Dietmar Kennepohl,
Zachary Sharrett, Duy Dang, Gamini Gunawardena, William Reusch, & William Reusch.

5.7.7 https://chem.libretexts.org/@go/page/31426
5.8: Racemic Mixtures and the Resolution of Enantiomers
 Objectives

After completing this section, you should be able to

1. describe a common process for separating a mixture of enantiomers.
2. explain why racemic mixtures do not rotate plane-polarized light.

 Key Terms
Make certain that you can define, and use in context, the key terms below.
racemic mixture (or racemate)
resolve

 Study Notes

A racemic mixture is a 50:50 mixture of two enantiomers. Because they are mirror images, each enantiomer rotates plane-
polarized light in an equal but opposite direction and is optically inactive. If the enantiomers are separated, the mixture is said
to have been resolved. A common experiment in the laboratory component of introductory organic chemistry involves the
resolution of a racemic mixture.
The dramatic biochemical consequences of chirality are illustrated by the use, in the 1950s, of the drug Thalidomide, a sedative
given to pregnant women to relieve morning sickness. It was later realized that while the (+)‑form of the molecule, was a safe
and effective sedative, the (−)‑form was an active teratogen. The drug caused numerous birth abnormalities when taken in the
early stages of pregnancy because it contained a mixture of the two forms.

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, 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 'Moscher's esters',
after Harry Stone Moscher, a chemist who pioneered the method at Stanford University.
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, 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.
Reversing the first reaction then leads to the separated enantiomers plus the recovered reagent.

Figure 5.8.1:

5.8.1 https://chem.libretexts.org/@go/page/31427
Many kinds of chemical and physical reactions, including salt formation, may be used to achieve the diastereomeric intermediates
needed for separation. Figure 5.8.1 illustrates this general principle by showing how a nut having a right-handed thread (R) could
serve as a "reagent" to discriminate and separate a mixture of right- and left-handed bolts of identical size and weight. Only the two
right-handed partners can interact to give a fully-threaded intermediate, so separation is fairly simple. The resolving moiety, i.e. the
nut, is then removed, leaving the bolts separated into their right and left-handed forms. Chemical reactions of enantiomers are
normally not so dramatically different, but a practical distinction is nevertheless possible.
Because the physical properties of enantiomers are identical, they seldom can be separated by simple physical methods, such as
fractional crystallization or distillation. It is only under the influence of another chiral substance that enantiomers behave
differently, and almost all methods of resolution of enantiomers are based upon this fact. We include here a discussion of the
primary methods of resolution.

Chiral Amines as Resolving Agents and Resolution of Racemic Acids

The most commonly used procedure for separating enantiomers is to convert them to a mixture of diastereomers that will have
different physical properties: melting point, boiling point, solubility, and so on (Section 5-5). For example, if you have a racemic or
(R)/(S) mixture of enantiomers of a carboxylic acid and convert this to a salt with a chiral amine base having the (R) configuration,
the salt will be a mixture of two diastereomers, ((R)-acid (R)-base) and ((S)-acid (R)-base). These diastereomeric salts are not
identical and they are not mirror images. Therefore they will differ to some degree in their physical properties, and a separation by
physical methods, such as crystallization, may be possible. If the diastereomeric salts can be completely separated, the carboxylic
acid regenerated from each salt will be either exclusively the (R) or the (S) enantiomer.
(R )-acid (R )-base pure (R )-carboxylic acid

(R )-carboxylic acid (R )-amine base (R )-acid (R )-base resolution regeneration

(S )-carboxylic acid (S )-acid (R )-base

racemic mixture diastereomers

(S )-acid (R )-base pure (S )-carboxylic acid

Resolution of chiral acids through the formation of diastereomeric salts requires adequate supplies of suitable chiral bases. Brucine,
strychnine, and quinine frequently are used for this purpose because they are readily available, naturally occurring chiral bases.
Simpler amines of synthetic origin, such as 2-amino-1-butanol, amphetamine, and 1-phenylethanamine, also can be used, but first
they must be resolved themselves.
NH2

* * *
OH
NH2 NH2

2-amino-1-butanol 1-phenyl-2-propanamine 1-phenylethanamine

(amphetamine)

N OH
H H
N
R H
H H N
R N O

O
O
R = H,strychnine quinine
(antimicrobial)
R = OCH3, brucine
(antimalarial)

 Worked Example 5.8.1

Show how (S)-1-phenylethylamine can be used to resolve a racemic mixture of lactic acid. Please draw all the structures
involved.

Answer

5.8.2 https://chem.libretexts.org/@go/page/31427
 O OH
C
O O H3N H C H
O OH C H3C
C C OH
C H H3 C
C H H3C pure (S )-lactic acid
H3C OH
OH
CH3
(S )-lactic acid C (S,R )-diastereomeric
H NH2 ammonium salt
+
(S )-1-phenylethylamine
O O H3N H
O OH C
C C
C H H3 C O OH
C OH H3C C
H3C OH
H
C OH
(R )-lactic acid (R,R )-diastereomeric H3 C
H
ammonium salt
pure (R )-lactic acid
racemic mixture
of lactic acid

Resolution of Racemic Bases

Chiral acids, such as (+)-tartaric acid, (-)-malic acid, (-)-mandelic acid, and (+)-camphor- 10-sulfonic acid, are used for the
resolution of a racemic base.
CO2H CO2H CH3
CO2H H3 C
CHOH CHOH SO3H
CHOH
CHOH CH2 O
C6 H5
CO2H CO2H

tartaric acid malic acid mandelic acid camphor-10-

(2,3-dihydroxy- (2-hydroxybutane- (2-hydroxy-2- sulfonic acid
butanedioic acid) dioic acid) phenylethanoic acid)

The principle is the same as for the resolution of a racemic acid with a chiral base, and the choice of acid will depend both on the
ease of separation of the diastereomeric salts and, of course, on the availability of the acid for the scale of the resolution involved.
Resolution methods of this kind can be tedious, because numerous recrystallizations in different solvents may be necessary to
progressively enrich the crystals in the less-soluble diastereomer. To determine when the resolution is complete, the mixture of
diastereomers is recrystallized until there is no further change in the measured optical rotation of the crystals. At this stage it is
hoped that the crystalline salt is a pure diastereomer from which one pure enantiomer can be recovered. The optical rotation of this
enantiomer will be a maximum value if it is "optically" pure because any amount of the other enantiomer could only reduce the
magnitude of the measured rotation α .

Resolution of Racemic Alcohols

To resolve a racemic alcohol, a chiral acid can be used to convert the alcohol to a mixture of diastereomeric esters. This is not as
generally useful as might be thought because esters tend to be liquids unless they are very high-molecularweight compounds. If the
diastereomeric esters are not crystalline, they must be separated by some other method than fractional crystallization (for instance,
by chromatography methods, Section 9-2). Two chiral acids that are useful resolving agents for alcohols are:

The most common method of resolving an alcohol is to convert it to a half-ester of a dicarboxylic acid, such as butanedioic
(succinic) or 1,2-benzenedicarboxylic (phthalic) acid, with the corresponding anhydride. The resulting half-ester has a free
carboxyl function and may then be resolvable with a chiral base, usually brucine:

5.8.3 https://chem.libretexts.org/@go/page/31427
 O O
CH3
* O
* CHOH brucine
+ O
CH2
HO
CH3
O
O
tartaric acid 1,2-benzenedicarboxylic half-ester
(2,3-dihydroxy- anhydride
butanedioic acid)

alkaline
hydrolysis D-2-butanol

separation by
crystallization
diastereomeric salts
alkaline
hydrolysis
L-2-butanol

Other Methods of Resolution

One of the major goals in the field of organic chemistry is the development of reagents with the property of "chiral recognition"
such that they can affect a clean separation of enantiomers in one operation without destroying either of the enantiomers. We have
not achieved that ideal yet, but it may not be far in the future. Chromatographic methods, whereby the stationary phase is a chiral
reagent that adsorbs one enantiomer more strongly than the other, have been used to resolve racemic compounds, but such
resolutions seldom have led to both pure enantiomers on a preparative scale. Other methods, called kinetic resolutions, are
excellent when applicable. The procedure takes advantage of differences in reaction rates of enantiomers with chiral reagents. One
enantiomer may react more rapidly, thereby leaving an excess of the other enantiomer behind. For example, racemic tartaric acid
can be resolved with the aid of certain penicillin molds that consume the dextrorotatory enantiomer faster than the levorotatory
enantiomer. As a result, almost pure (-)-tartaric acid can be recovered from the mixture:
(±)-tartaric acid + mold → (-)-tartaric acid + more mold
The crystallization procedure employed by Pasteur for his classical resolution of (±)-tartaric acid (Section 5.4) has been successful
only in a very few cases. This procedure depends on the formation of individual crystals of each enantiomer. Thus if the
crystallization of sodium ammonium tartrate is carried out below 27", the usual racemate salt does not form; a mixture of crystals
of the (+) and (-) salts forms instead. The two different kinds of crystals, which are related as an object to its mirror image, can be
separated manually with the aid of a microscope and subsequently may be converted to the tartaric acid enantiomers by strong acid.
A variation on this method of resolution is the seeding of a saturated solution of a racemic mixture with crystals of one pure
enantiomer in the hope of causing crystallization of just that one enantiomer, thereby leaving the other in solution. Unfortunately,
very few practical resolutions have been achieved in this way.

Predicating the Chirality of the Product of a Reaction

It important to understand the changes in chirality which occur during the formation of product during a reaction. A chiral reaction
product, has the possibility of forming multiple stereoisomers which all need to be considered. Changes in chirality, if possible, will
be discussed with each individual reaction as this textbook moves forward. Some possible situations which can occur are:
A new chiral carbon is formed during a reaction. This commonly occurs when an sp2 hybridized carbon in the reactant is
converted to sp3 hybridized chiral carbon in the product. When this occurs, a racemic mixture of the new chiral carbon is
formed.
A chiral carbon is lost during a reaction. This commonly occurs when an sp3 hybridized chiral carbon in the reactant is
converted to either a sp2 or sp hybridized carbon in the product.
An enantiomerically pure starting material is converted to a racemic mixture in the product. This commonly occurs when
a sp3 hybridized chiral carbon is temporarily converted to an sp2 hybridized carbon during a reaction's mechanism. The chiral
carbon is reformed as a racemic mixture.
Chiral carbons remain unchanged during a reaction. If a chiral carbon is not directly involved in a reaction, it will move
from a reactant to a product unchanged.
Determining if a chiral carbon is involved in a given reaction is vital for determining which of these four situations is occurring.

5.8.4 https://chem.libretexts.org/@go/page/31427
  Worked Example 5.8.2

The following reaction involves the conversion of a carboxylic acid reacting with an alcohol to form an ester. If a pure sample
of (R)-2-methylbutanoic acid is reacted with methanol to form an ester, what would be the stereochemistry of the product?
O O
acid
+ HO R’ + H2O
C C R’
R OH R O
carboxylic acid alcohol ester

Answer
First it is important to identify the location of the chiral carbon and determine if it is directly involved in the reaction. In
this case, the chiral carbon is not involved so the stereochemistry will be carried over into the product unchanged.
O O
H2 H2
acid
C * C + HO CH3 C * C CH3 + H2 O
H3C C OH H3C C O
H CH3 H CH3
(R )-2-methylbutanoic methanol methyl (R )-2-methyl
acid butanoate

 Exercise 5.8.1

Indicate the reagents you could use to resolve the following compounds. Show the reactions involved and specify the physical
method you believe would be the best to separate the diastereomers of 1 -phenyl-2-propanamine.

Answer
You could react the 1-phenyl-2-propanamine racemic mixture with a chiral acid such as (+)-tartaric acid (R, R). The
reaction will produce a mixture of diastereomeric salts (i.e. R, R, R and S, R, R). You can separate the diastereomers through
crystallization and treat the salt with a strong base (e.g. KOH) to recover the pure enantiomeric amine.

 Exercise 5.8.2

Indicate the reagents you would use to resolve the following and discuss the reactions involved and specify the physical
method you believe would be the best to separate the diastereomers of 2,3-pentadienedioic acid.

Answer
You could react the 2,3-pentadienedioic acid mixture with a chiral base such as (R)‑1‑phenylethylamine. The reaction will
produce a mixture of diastereomeric salts. Separate the diastereomers through crystallization and treat the resulting salt with
strong acid (e.g. HCl) to recover the pure enantiomeric acid.

 Exercise 5.8.3

Indicate the reagents you would use to resolve the following and discuss the reactions involved and specify the physical
method you believe would be the best to separate the diastereomers of 1 -phenylethanol.

Answer
You could react the 1-phenylethanol mixture with 1,2-benzenedicarboxylic anhydride. The reaction will produce a mixture
of diastereomeric salts. You could then separate the diastereomers through crystallization and then alkaline hydrolysis
treatment should recover the pure enantiomeric alcohol.

5.8: Racemic Mixtures and the Resolution of Enantiomers is shared under a CC BY-SA 4.0 license and was authored, remixed, and/or curated by
Steven Farmer, Dietmar Kennepohl, Zachary Sharrett, Layne Morsch, John Roberts, Marjorie C. Caserio, & Marjorie C. Caserio.

5.8.5 https://chem.libretexts.org/@go/page/31427
5.9: A Review of Isomerism
 Objective

After completing this section, you should be able to explain the differences among constitutional (structural) isomers and
stereoisomers (geometric isomers).

 Key Terms

Make certain that you can define, and use in context, the key terms below.
constitutional
(structural) isomers
stereoisomers

The following flow chart can be used to identify the relationship of two compounds with respect to isomerization:

Figure 5.9.1 : Different types of isomers. When using the flow chart, it is really important to remember that each decision on the
flow chart is related to comparing two molecules, ie. it doesn't make sense to ask "what is compound A", but it does make sense to
ask "how are compounds A and B related"? A molecule may be the enantiomer of another molecule, but a diastereomer of another.
(CC-BY-SA 4.0; Mark Coster via StackExchange)

Conformational Isomers
The C–C single bonds in ethane, propane, and other alkanes are formed by the overlap of an sp3 hybrid orbital on one carbon atom
with an sp3 hybrid orbital on another carbon atom, forming a σ bond. Each sp3 hybrid orbital is cylindrically symmetrical (all cross-
sections are circles), resulting in a carbon–carbon single bond that is also cylindrically symmetrical about the C–C axis. Because
rotation about the carbon–carbon single bond can occur without changing the overlap of the sp3 hybrid orbitals, there is no
significant electronic energy barrier to rotation. Consequently, many different arrangements of the atoms are possible, each
corresponding to different degrees of rotation. Differences in three-dimensional structure resulting from rotation about a σ bond are
called differences in conformation, and each different arrangement is called a conformational isomer (or conformer).

Conformational Isomers of Pentane

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Structural Isomers
Unlike conformational isomers, which do not differ in connectivity, structural isomers differ in connectivity, as illustrated here for
1-propanol and 2-propanol. Although these two alcohols have the same molecular formula (C3H8O), the position of the –OH group
differs, which leads to differences in their physical and chemical properties.
H H H
H C C C OH
H H H
1-propanol (n-propanol)

H OH H
H C C C H
H H H
2-propanol (isopropanol)

In the conversion of one structural isomer to another, at least one bond must be broken and reformed at a different position in the
molecule. Consider, for example, the following five structures represented by the formula C5H12:
CH3
CH3CH2CH2CH2CH3 CH3CHCH2CH3 CH3CH2CHCH3 CH3CH2CH2CH2CH3 CH3CCH3
CH3 CH3 CH3
(a) (b) (c) (d) (e)

Of these structures, (a) and (d) represent the same compound, as do (b) and (c). No bonds have been broken and reformed; the
molecules are simply rotated about a 180° vertical axis. Only three—n-pentane (a) and (d), 2-methylbutane (b) and (c), and 2,2-
dimethylpropane (e)—are structural isomers. Because no bonds are broken in going from (a) to (d) or from (b) to (c), these
alternative representations are not structural isomers. The three structural isomers—either (a) or (d), either (b) or (c), and (e)—have
distinct physical and chemical properties.

Stereoisomers
Stereoisomers have the same connectivity in their atoms but a different arrangement in three-dimensional space. There are
different classifications of stereoisomers depending on how the arrangements differ from one another. Notice that in the structural
isomers, there was some difference in the connection of atoms. For example, 1-butene has a double bond followed by two single
bonds while 2-butene has a single bond, then a double bond, then a single bond. A stereoisomer will have the same connectivity
among all atoms in the molecule.

Geometric Isomers
With a molecule such as 2-butene, a different type of isomerism called geometric isomerism can be observed. Geometric isomers
are isomers in which the order of atom bonding is the same but the arrangement of atoms in space is different. The double bond in
an alkene is not free to rotate because of the nature of the bond. Therefore, there are two different ways to construct the 2-butene
molecule (see figure below). The image below shows the two geometric isomers, called cis-2-butene and trans-2-butene.
H H
cis -2-butene C C
H 3C CH3

H CH3
trans -2-butene C C
H 3C H

Geometric Isomers of 2-Butene

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The cis isomer has the two single hydrogen atoms on the same side of the molecule, while the trans isomer has them on opposite
sides of the molecule. In both molecules, the bonding order of the atoms is the same. In order for geometric isomers to exist, there
must be a rigid structure in the molecule to prevent free rotation around a bond. This occurs with a double bond or a ring. In
addition, the two carbon atoms must each have two different groups attached in order for there to be geometric isomers. Propene
(see figure below) has no geometric isomers because one of the carbon atoms (the one on the far left) involved in the double bond
has two single hydrogens bonded to it.
H H
H C H
C C
H H

Physical and chemical properties of geometric isomers are generally different. As with alkenes, alkynes display structural
isomerism beginning with 1-butyne and 2-butyne. However, there are no geometric isomers with alkynes because there is only one
other group bonded to the carbon atoms that are involved in the triple bond.

Optical Isomers
Stereoisomers that are not geometric isomers are known as optical isomers. Optical isomers differ in the placement of substituted
groups around one or more atoms of the molecule. They were given their name because of their interactions with plane-polarized
light. Optical isomers are labeled enantiomers or diastereomers.
Enantiomers are non-superimposable mirror images. A common example of a pair of enantiomers is your hands. Your hands are
mirror images of one another but no matter how you turn, twist, or rotate your hands, they are not superimposable.

Two models that are mirror images and superimposable.

Since they are superimposable, they are the same molecule and are not isomers.

Your hands and some molecules are mirror images but are not superimposable.
These pairs of molecules are called enantiomers.
Objects that have non-superimposable mirror images are called chiral. When examining a molecule, carbon atoms with four
unique groups attached are considered chiral. Look at the figure below to see an example of a chiral molecule. Note that we have to
look beyond the first atom attached to the central carbon atom. The four circles indicate the four unique groups attached to the
central carbon atom, which is chiral.

H
HO C CH2CH3
CH3

A chiral carbon has four unique groups attached to it

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Another type of optical isomer are diastereomers, which are non-mirror image optical isomers. Diastereomers have a different
arrangement around one or more atoms while some of the atoms have the same arrangement. As shown in the figure below, note
that the orientation of groups on the first and third carbons are different but the second one remains the same so they are not the
same molecule. The solid wedge indicates a group coming out of the page/screen towards you and the dashed line indicates that a
group is going away from you "behind" the page/screen.
H OH H F HO H F H
C C C C
H3 C C CH3 H3C C CH3
H OH H OH

Diastereomers differ at one or more atom. These molecules are not mirror images and they are not superimposable.
They are optical isomers because they have the same connectivity between atoms but a different arrangement of substituent
groups.
Epimers are a sub-group of diastereomers that differ at only one location. All epimers are diastereomers but not all diastereomers
are epimers.
H OH H F H OH F H
C C C C
H 3C C CH3 H 3C C CH3
H OH H OH

Epimers have a different arrangement around one atom, while arrangements around the other atoms are the same

stereoisomers

diastereomers

enantiomers
epimers

Diagram showing the division of stereoisomers (also known as optical isomers)

 Exercise 5.9.1

What kind of isomers are the following pairs?

a) and

H3C OH O
b) C and H C CH3
H2 3

c) and
Br Br

Answer
a. Since both structures have the same formula (C6H12) and they have the same connectivity, but are in a different
arrangement of the atoms in space, they are conformational isomers.
b. Since both structures have the same formula (C2H6O) but different connectivity, they are structural isomers.

5.9.4 https://chem.libretexts.org/@go/page/31428
 c. Since both structures have the same formula (C3H9Br) and the same connectivity but the structure on the left has R
stereochemistry and the structure on the right has S stereochemistry, they are stereoisomers called enantiomers.

 Exercise 5.9.2

What kind of isomers are the following pairs?

a) and

Br Br
b) and
CH3 CH3

OH OH

c) and

F F

Answer
a) Since both structures have the same formula (C2H6O) but different connectivity of where the double bond is, they are
structural isomers.
b) Both structures have the same formula and the same connectivity but the structure on the left has (R,S) stereochemistry
and the structure on the right has (S,S) stereochemistry, they are stereoisomers that are diastereomers.
(R ) (S )
Br Br

(S ) CH3 (S ) CH3

c) Both structures and have the same connectivity but their stereochemistry differs so they are stereoisomers. Since the one
on the left is (R,S) and the one on the right is (S,R), they are non-super imposable mirror images of each other and
enantiomers.
OH OH
(R ) (S )

(S ) (R )
F F

 Exercise 5.9.3

What is the relationship between the following pairs?

c) (R) – 2 chlorohexane & 1-chlorohexane
a) and
d) (2R, 3R) dichlorohexane & (2S, 3R) dichlorohexane
Br Br Br Br

Answer
b) and a) Both structures have the same connectivity and same chemical formula and
when you rotate the structure on the right you can see that these are the same
compound both with (R,S) stereochemistry.

and =
Br Br Br Br Br Br

b) ) Since both structures have the same formula (C4H8) and the same connectivity they are stereoisomers since they differ
in what is known as cis/trans isomerism (covered more in Ch 7).Due to the pi bond between carbons 2 & 3, there is not free

5.9.5 https://chem.libretexts.org/@go/page/31428
 rotation between the C2-C3 bond so the structure on the left has the carbon chains on the same side of the double bond (cis)
and the structure on the right has the carbon chains on opposite sides of the double bond (trans).

and

c) Looking at the structures below, you can see that they have the same formula (C6H13Cl) and different connectivity, so
they are structural isomers.
Cl
and Cl

d) Looking at the structures below, you can see that they have the same formula (C6H12Br2) and the same connectivity, but
the structure on the left is (R,R) and the structure on the right is (S,R) so since they differ by only one stereocenter, they are
stereoisomers that are diastereomers (& epimers in this case).
Br Br
(R ) (S )
and
(R ) (R )
Br Br

5.9: A Review of Isomerism is shared under a CC BY-SA 4.0 license and was authored, remixed, and/or curated by Steven Farmer, Dietmar
Kennepohl, Zachary Sharrett, William Reusch, & William Reusch.

5.9.6 https://chem.libretexts.org/@go/page/31428
5.10: Chirality at Nitrogen, Phosphorus, and Sulfur
 Objectives

After completing this section, you should be able to

1. recognize that atoms other than carbon can be chiral centres.
2. explain why enantiomers of compounds such as ethylmethylamine cannot normally be isolated.

 Study Notes
The first example of a resolvable compound containing a chiral nitrogen atom was resolved by William Pope and Stanley
Peachey in 1899. It had the structure shown below.
a resolvable compound with a chiral nitrogen centre

Chiral sulfoxides find application in certain drugs such as esomeprazole and armodafinil and are a good example of a
stereogenic sulfur center.
O

NH2
S
O

armodafinil

Chirality at Nitrogen
Due to their tetrahedral configuration, amines with three different substituents are chiral. The R and S enantiomeric forms of chiral
amines cannot be resolved due to their rapid interconversion by a process called pyramidal or nitrogen inversion. During the
inversion, the sp3 hybridized amine momentarily rehybridizes to a sp2 hybridized, trigonal planar, transition state where the lone
pair electrons occupy a p orbital. The nitrogen then returns to tetrahedral sp3 hybridization causing the lone pair electrons to enter
to a hybrid orbital on the opposite side of the nitrogen. During this process substituents invert to form the enantiomer, analogous to
the Walden inversion seen in SN2 reactions. The thermodynamic barrier for this inversion (~25 kJ/mol) is low enough to allow
rapid inversion at room temperature, leading to a mixture of interconverting R and S configurations. At room temperature a
nitrogen atom exists as a racemic mixture of R and S configurations.

R' R R' R R R'

N N N
fast fast
R'' R’’ R''

sp3-hybridized sp2-hybridized sp3-hybridized

(tetrahedral) (trigonal planar) (tetrahedral)

Quaternary amines lack lone pair electrons and therefore do not undergo pyramidal inversions. Quaternary amines with four
different substituents are chiral and are readily resolved into separate enantiomers.

R' R R R'
N R''' R''' N
R'' R''

enantiomers of a chiral
quaternary amine

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  Example 5.10.1

The Enantiomers of a chiral quaternary amine.

mirror

N CH3 H3 C N
CH2CH3 H3CH2C

(R )-configuration (S )-configuration

Chirality at Phosphorus
Trivalent phosphorus compounds called phosphines have a tetrahedral electron-group geometry which makes them structurally
analogous to amines. The rate of inversion for phosphines are so much slower than amines that chiral phosphines can be isolated.
In this case the set of lone pair electrons are considered a substituent and given the lowest Cahn-Ingold-Prelog priority.
mirror

P CH H 3C P
3
CH2CH3 H3CH2C

(R )-configuration (S )-configuration

enantiomers of
ethylmethylphenylphosphine

The phosphorus center of phosphate ions and organic phosphate esters is also tetrahedral, and thus potentially a stereocenter. In
order to investigate the stereochemistry of reactions at the phosphate center, 17O and 18O isotopes of oxygen (the ‘normal’ isotope
is 16O) can be incorporated to create chiral phosphate groups. Phosphate triesters are chiral if the all four substituent groups are
different (including the carbonyl oxygen).
18
O O O

O P O O P OR RO P OR''
16
17
O O R'O

phosphate labeled phosphate ester a chiral phosphate triester

(achiral) (chiral)

Chirality at Sulfur
Trivalent sulfur compounds called sulfonium salts (R3S+) have a tetrahedral electron-group geometry similar to amines and can be
chiral if the R groups are all different. In a similar fashion as phosphorus, the inversion rates are slow enough for chiral sulfonium
salts to be isolated. Here again the set of lone pair electrons are considered a substituent and given the lowest CIP priority.
Sulfonium salts will be discussed in greater detail in Section 18.8.
lowest priority

S R''
R
R'
a chiral sulfur in the
form of a sulfonium ion

An excellent example of a chiral sulfonium salt in biological systems is the coenzyme (S)-adenosylmethionine (SAM). The
presence of a sulfonium allows SAM to be a biological methyl group donor in many metabolic pathways. Note that SAM has an (S)
configuration at the sulfur atom.

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 NH2
(S )-configuration
N
N
O CH3 N N
S
O O
NH3
OH OH
(S )-S-adenosylmethionine

The sulfur in sulfoxides (R'SOR'') can be chiral if both R groups are different. Here again the inversion rate is slow enough to allow
chiral sulfoxides to be isolated. An excellent example is methyl phenyl sulfoxide. Sulfoxides will also be discussed in greater detail
in Section 18.8.
mirror

O
S CH
3 H3C S O

(R )-configuration (S )-configuration

enantiomers of methyl phenyl sulfoxide

5.10: Chirality at Nitrogen, Phosphorus, and Sulfur is shared under a CC BY-SA 4.0 license and was authored, remixed, and/or curated by Steven
Farmer, Dietmar Kennepohl, Tim Soderberg, William Reusch, Dr. Dietmar Kennepohl, & Dr. Dietmar Kennepohl.

5.10.3 https://chem.libretexts.org/@go/page/31429
5.11: Prochirality
 Objectives

After completing this section, you should be able to

1. identify a compound as being prochiral.
2. identify the Re and Si faces of prochiral sp2 centre.
3. identify atoms (or groups of atoms) as pro-R or pro-S on a prochiral sp3 centre.

 Key Terms
Make certain that you can define, and use in context, the key terms below.
prochiral
pro-R
pro-S
Re
Si

Prochiral Carbons
When a tetrahedral carbon can be converted to a chiral center by changing only one of the attached groups, it is referred to as a
‘prochiral' carbon. The two hydrogens on the prochiral carbon can be described as 'prochiral hydrogens'.
prochiral hydrogens

H H H D
change H to D
R R’ R R’

prochiral carbon chiral carbon

Note that if, in a 'thought experiment', we were to change either one of the prochiral hydrogens on a prochiral carbon center to a
deuterium (the 2H isotope of hydrogen), the carbon would now have four different substituents and thus would be a chiral center.
Prochirality is an important concept in biological chemistry, because enzymes can distinguish between the two ‘identical’ groups
bound to a prochiral carbon center due to the fact that they occupy different regions in three-dimensional space. Consider the
isomerization reaction below, which is part of the biosynthesis of isoprenoid compounds. We do not need to understand the reaction
itself (it will be covered in chapter 14); all we need to recognize at this point is that the isomerase enzyme is able to distinguish
between the prochiral 'red' and the 'blue' hydrogens on the isopentenyl diphosphate (IPP) substrate. In the course of the left to right
reaction, IPP specifically loses the 'red' hydrogen and keeps the 'blue' one.
H H H
O O O O O O
P P P P
O O O O O O O O

isopentenyl diphosphate dimethylallyl diphosphate

Prochiral hydrogens can be unambiguously designated using a variation on the R/S system for labeling chiral centers. For the sake
of clarity, we'll look at a very simple molecule, ethanol, to explain this system. To name the 'red' and 'blue' prochiral hydrogens on
ethanol, we need to engage in a thought experiment. If we, in our imagination, were to arbitrarily change red H to a deuterium, the
molecule would now be chiral and the chiral carbon would have the R configuration (D has a higher priority than H).
change H to D
H H stereocenter is now (R ) H D
(R )
H3 C OH H3 C OH

Hs HR

H3C OH

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For this reason, we can refer to the red H as the pro-R hydrogen of ethanol, and label it HR. Conversely, if we change the blue H to
D and leave red H as a hydrogen, the configuration of the molecule would be S, so we can refer to blue H as the pro-S hydrogen of
ethanol, and label it HS.
Looking back at our isoprenoid biosynthesis example, we see that it is specifically the pro-R hydrogen that the isopentenyl
diphosphate substrate loses in the reaction.
HS HR H
O O O O O O
P P P P
O O O O O O O O

isopentenyl diphosphate dimethylallyl diphosphate

Prochiral hydrogens can be designated either enantiotopic or diastereotopic. If either HR or HS on ethanol were replaced by a
deuterium, the two resulting isomers would be enantiomers (because there are no other stereocenters anywhere on the molecule).
CH3 CH3 CH3
HR C H C(S ) D C(R )
OH OH OH
HS D H

enantiotopic
hydrogens enantiomers

Thus, these two hydrogens are referred to as enantiotopic.

In (R)-glyceraldehyde-3-phosphate ((R)-GAP), however, we see something different:
diastereotopic
hydrogens

HR HS O H D O D H O
(R ) (R ) (R )
PO H PO (S ) H PO (R ) H
OH OH OH
(R )-GAP
diastereomers

R)-GAP already has one chiral center. If either of the prochiral hydrogens HR or HS is replaced by a deuterium, a second chiral
center is created, and the two resulting molecules will be diastereomers (one is S,R, one is R,R). Thus, in this molecule, HR and HS
are referred to as diastereotopic hydrogens.
Finally, hydrogens that can be designated neither enantiotopic nor diastereotopic are called homotopic. If a homotopic hydrogen is
replaced by deuterium, a chiral center is not created. The three hydrogen atoms on the methyl (CH3) group of ethanol (and on any
methyl group) are homotopic. An enzyme cannot distinguish among homotopic hydrogens.
H homotopic hydrogens
H
C H
HR C
OH
HS

 Example 5.11.1

Identify in the molecules below all pairs/groups of hydrogens that are homotopic, enantiotopic, or diastereotopic. When
appropriate, label prochiral hydrogens as HR or HS.

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 O
a) b)
H OP
N
O
O N CO2

H O
dihydroorotate phosphoenolpyruvate
(a nucleotide biosynthesis intermediate) (a glycolysis intermediate)

O
c) d) C O
CO2
O 2C H 3C C
O
succinate pyruvate
(a citric acid cycle intermediate) (endpoint of glycolysis)

Answer
(no pro-R or pro-S
designation is possible)
O
a) HR diastereotopic b)
H H OP
N HS
diastereotopic
O
O N H CO2

H O

enantiotopic
HR HS O
c) d) C O
CO2
O2 C H3 C C
HS HR homotopic O
enantiotopic

Groups other than hydrogens can be considered prochiral. The alcohol below has two prochiral methyl groups - the red one is pro-
R, the blue is pro-S. How do we make these designations? Simple - just arbitrarily assign the red methyl a higher priority than the
blue, and the compound now has the R configuration - therefore red methyl is pro-R.
methyl B (pro-S)
OH
H3C C
CH2CH3
H 3C

methyl A (pro-R)

Citrate is another example. The central carbon is a prochiral center with two 'arms' that are identical except that one can be
designated pro-R and the other pro-S.
HO CO2
O 2C CO2

pro-R arm pro-S arm

citrate

In an isomerization reaction of the citric acid (Krebs) cycle, a hydroxide is shifted specifically to the pro-R arm of citrate to form
isocitrate: again, the enzyme catalyzing the reaction distinguishes between the two prochiral arms of the substrate (we will study
this reaction in chapter 13).

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 CO2 CO2
pro-S arm pro-R arm

O2 C OH
(draw from a different

=
perspective)
CO2
HO CO2 O2 C CO2
O2 C CO2
pro-R arm pro-S arm OH

citrate isocitrate
(hydroxide moved
specifically to the
pro-R arm)

 Exercise 5.11.1

Assign pro-R and pro-S designations to all prochiral groups in the amino acid leucine. (Hint: there are two pairs of prochiral
groups!). Are these prochiral groups diastereotopic or enantiotopic?

O
H3N
O
leucine

Answer
pro-R
H CH3
HR
HS b CH pro-S
a 3
O
H 3N
O

Prochiral Carbonyl and Imine Groups

Trigonal planar, sp2-hybridized carbons are not, as we well know, chiral centers– but they can be prochiral centers if they are
bonded to three different substitutuents. We (and the enzymes that catalyze reactions for which they are substrates) can distinguish
between the two planar ‘faces’ of a prochiral sp2 - hybridized group. These faces are designated by the terms re and si. To
determine which is the re and which is the si face of a planar organic group, we simply use the same priority rankings that we are
familiar with from the R/S system, and trace a circle: re is clockwise and si is counterclockwise.

1
1 1
re face si face

3 2 3 2 2 3

looking at the re face looking at the si face

When the two groups adjacent to a carbonyl (C=O) are not the same, we can distinguish between the re and si 'faces' of the planar
structure. The concept of a trigonal planar group having two distinct faces comes into play when we consider the stereochemical
outcome of a nucleophilic addition reaction. Nucleophilic additions to carbonyls will be covered in greater detail in Chapter 19.
Notice that in the course of a carbonyl addition reaction, the hybridization of the carbonyl carbon changes from sp2 to sp3, meaning
that the bond geometry changes from trigonal planar to tetrahedral. If the two R groups are not equivalent, then a chiral center is
created upon addition of the nucleophile. The configuration of the new chiral center depends upon which side of the carbonyl plane
the nucleophile attacks from. Reactions of this type often result in a 50:50 racemic mixture of stereoisomers, but it is also possible
that one stereoisomer may be more abundant, depending on the structure of the reactants and the conditions under which the
reaction takes place.

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 H OH OH H
O O
C R' R' C
Nu R' C Nu Nu C Nu
R R R R' R
attack at re face enantiomers attack at si face

Note: R is higher priority than R’

Below, for example, we are looking down on the re face of the ketone group in pyruvate. If we flipped the molecule over, we would
be looking at the si face of the ketone group. Note that the carboxylate group does not have re and si faces, because two of the three
substituents on that carbon are identical (when the two resonance forms of carboxylate are taken into account).
priority #1

O
C O
priority #3 H3 C C priority #2

As we will see in chapter 10, enzymes which catalyze reactions at carbonyl carbons act specifically from one side or the other.

HO CO2 HS HR O HO CO2
H O

NH2 NH2
+ +
(R )
H2C OH N H 2C OH N

O R HO H R
looking at the si face
of the ketone

We need not worry about understanding the details of the reaction pictured above at this point, other than to notice the
stereochemistry involved. The pro-R hydrogen (along with the two electrons in the C-H bond) is transferred to the si face of the
ketone (in green), forming, in this particular example, an alcohol with the R configuration. If the transfer had taken place at the re
face of the ketone, the result would have been an alcohol with the S configuration.

 Exercise 5.11.2

For each of the carbonyl groups in uracil, state whether we are looking at the re or the si face in the structural drawing below.
O
H
N

N O
H
uracil

Answer
1

O
H looking at the re face
3
N 2 of this carbonyl group

N O
H

O
2
H
N looking at the si face
of this carbonyl group
N O
3 1
H

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 Exercise 5.11.3

a) State which of the following hydrogen atoms are pro-R or pro-S.

Ha Hb Ha Hb
HO OH
HO H H2N H

b) Identify which side is Re or Si.

C
A

O H OH

OH

B
D

Answer
a) Left compound: Ha = pro-S and Hb = pro-R; Right compound: Ha = pro-R and Hb = pro-S
b) A – Re; B – Si; C – Re; D – Si\)

 Exercise 5.11.4

State whether the H's indicated below are pro-R or pro-S for the following structures.
a) Ha Hb b) Ha Hb

HO H O

Answer
a) Ha is pro-R; Hb is pro-S
Ha is pro-R; Hb is pro-S

 Exercise 5.11.5
In the structures below, determine if the H's are homotopic, enantiotopic, or diastereotopic.
a) Ha Hb b) Ha Hb

HO H O

Answer
In a), the CH2 is diastereotopic since there is another chiral center on the molecule. Both CH3's are homotopic since
replacing one of them doesn't create a chiral center.
IN b), the CH2's are enantiotopic since it would create the only chiral center on the molecule. Both CH3's are homotopic
since replacing one of them doesn't create a chiral center.
diastereotopic enantiotopic enantiotopic
a) b)
Ha Hb H2 H a Hb
CH3 C
H 3C H 3C CH3
homotopic
HO H homotopic homotopic
homotopic O

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  Exercise 5.11.6
State whether you are looking down at the molecule from the re face or si face.
a) b)
O HOH2C H

HOH2C CH2CH3 H H

Answer
a. You are looking at the si face. The re face would be if you were facing the molecule from the back.
b. You are looking at the re face. The si face would be if you were facing the molecule from the back.

5.11: Prochirality is shared under a CC BY-SA 4.0 license and was authored, remixed, and/or curated by Steven Farmer, Dietmar Kennepohl,
Zachary Sharrett, & Zachary Sharrett.
Current page by Dietmar Kennepohl, Steven Farmer, Zachary Sharrett is licensed CC BY-SA 4.0.
3.12: Prochirality by Tim Soderberg is licensed CC BY-NC-SA 4.0. Original source:
https://digitalcommons.morris.umn.edu/chem_facpubs/1/.

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5.12: Chirality in Nature and Chiral Environments
 Objective

After completing this section, you should be able to explain how chiral molecules in nature can have such dramatically
different biological properties.

Some Chiral Organic Molecules

There are a number of important biomolecules that could occur as enantiomers, including amino acids and sugars. In most cases,
only one enantiomer occurs naturally (although some fungi, for example, are able to produce mirror-image forms of these
compounds). We will look later at some of these biomolecules, but first we will look at a compound that occurs naturally in both
enantiomeric forms.
Carvone is a secondary metabolite. That means it is a naturally-occurring compound that is not directly connected to the very basic
functions of a cell, such as self-replication or the production of energy. The role of secondary metabolites in nature is often difficult
to determine. However, these compounds often play roles in self-defense, acting as deterrents against competitor species in a sort of
small-scale chemical warfare scenario. They are also frequently used in communications; this role has been studied most
extensively among insects, which use lots of compounds to send information to each other.
CH3 CH3
O O

H CH3 H3C H
H2 C CH2

(S )-carvone (R )-carvone
oil at 25 °C oil at 25 °C
bp: 230-231 °C bp: 230-231 °C
d: 0.965 g/mL d: 0.965 g/mL
n: 1.4988 n: 1.4988
insol H2O, misc EtOH, MeOH insol H2O, misc EtOH, MeOH
[⍺]D = +61.2° [⍺]D= −62.46°

Figure 5.12.1 : The two naturally-occurring enantiomers of carvone.

Carvone is produced in two enantiomeric forms. One of these forms, called (-)-carvone, is found in mint leaves, and it is a principal
contributor to the distinctive odor of mint. The other form, (+)-carvone, is found in caraway seeds. This form has a very different
smell, and is typically used to flavor rye bread and other Eastern European foods.
Note that (+)-carvone is another name for (S)-carvone. The (+) designation is based on its positive optical rotation value, which is
experimentally measured. This means the (-)-carvone is (R)-carvone and would have a negative optical rotation value.
How different, exactly, are these two compounds, (+)- and (-)-carvone? Are they completely different isomers, with different
physical properties? In most ways, the answer is no. These two compounds have the same appearance (colorless oil), the same
boiling point (230 °C), the same refractive index (1.499) and specific gravity (0.965). However, they have optical rotations that are
almost exactly opposite values.
Two enantiomers have the same physical properties.
Enantiomers have opposite optical rotations.
Clearly they have different biological properties; since they have slightly different odors, they must fit into slightly different nasal
receptors, signaling to the brain whether the person next to you is chewing a stick of gum or a piece of rye bread. This is much like
how a left hand only fits into a left handed baseball glove and not into a right handed one. Receptors which allow for a biological
effect, in this case to perceive a certain smell, are often chiral and will only allow one enantiomer of a chiral substrate to fit. An
example of this is shown in the figure below. The receptor as a complementary three-dimension shape to allow the R configuration
of the chiral substrate to fit. When the S configuration of the chiral substrate attempts to fit the configuration does not match that of
the receptor as shown in the second drawing where the bottom two groups do not fit the receptor site.

5.12.1 https://chem.libretexts.org/@go/page/31431
 C + C

Chiral molecule Receptor Molecule Fits

(R Configuration)

C + C

Chiral molecule Receptor Molecule Does

(S Configuration) Not Fit

Chiral Environments
In the previous section, enzymes were shown to be capable of converting a prochiral substrate into a single enantiomer product.
Enzymes can provides such an effect because they create a chiral environment. The figure below shows a prochiral substrate. The
magenta and blue balls represent substituents while the two green balls represent two of the same substituent which is available for
a given reaction. One of these substituents is pro-R and the other is pro-S. Without the presence of a chiral environment the two
green substituents are chemically identical. However, as the prochiral molecule interacts with the chiral environment provided by
an enzyme the two green substituents become chemically distinct. Despite being achiral, the prochiral molecule can only interact
with the chiral environment in one specific position. The figure below shows that the pro-S green substituent of the prochiral
molecule is protected by the enzyme, while the pro-R green substituent is exposed and can undergo a reaction. In this case the
enzyme would provide a product that is predominantly the R enantiomer.

pro-R pro-S
C + C

Prochiral molecule Chiral environment Molecule Fits

from an enzyme

 Exercise 5.12.1

The following are three molecules found in nature. Please identify four chiral centers in each, mark them with asterisks, and
identify each center as having a R or S configuration. Each molecule contains more than four chiral centers.
a) The following is the structure of dysinosin A, a potent thrombin inhibitor that consequently prevents blood clotting.
H
HO O

HO N HN
H
O
N NH
H 3C
HN O
CH3 H 2N

H3CO
O
O
S
OH
O

b) Ginkgolide B (below) is a secondary metabolite of the ginkgo tree, extracts of which are used in Chinese medicine.

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 O
O
HO H
HO

O O O
H H
O
HO
O

c) Sanglifehrin A, shown below, is produced by a bacteria that may be found in the soil of coffee plantations in Malawi. It is
also a promising candidate for the treatment of organ transplant patients owing to its potent immuno-suppressant activity.
OH OH O

HO

O OH O
O HN O
NH H H
N N
O N
O O OH

OH

Answer
a)
H
HO (S ) O
*
*(R )
(R )
* *
HO (S* ) N (S ) HN
H
O
* (R ) N NH
H3C
HN O
CH3 H2N
* (R )
H3CO
O
O
S
OH
O

b)
O
(R ) O
HO * (S ) H
HO (R ) (R ) * *(R )
* *
O O (S ) O *(S )
* (R )
H * (R* ) (R*) H
(S )
* O
HO
O

c)
OH OH O
(S ) (S ) (R )
HO (S ) (S ) (S )
* * * * (S* )
* *) *
(R* ) *
(S )
(R
(S ) O OH O
* O HN O
H H
(R* ) NH (S )
N (S )
N
(S )
* (R )
(R ) (S ) O * N * *
*
* O O OH

OH

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 O

N * O
NH
O O
Figure \(\PageIndex{2}\): Thalidomide.
There are other reasons that we might concern ourselves with an understanding of enantiomers, apart from dietary and olfactory
preferences. Perhaps the most dramatic example of the importance of enantiomers can be found in the case of thalidomide.
Thalidomide was a drug commonly prescribed during the 1950's and 1960's in order to alleviate nausea and other symptoms of
morning sickness. In fact, only one enantiomer of thalidomide had any therapeutic effect in this regard. The other enantiomer, apart
from being therapeutically useless in this application, was subsequently found to be a teratogen, meaning it produces pronounced
birth defects. This was obviously not a good thing to prescribe to pregnant women. Workers in the pharmaceutical industry are now
much more aware of these kinds of consequences, although of course not all problems with drugs go undetected even through the
extensive clinical trials required in the United States. Since the era of thalidomide, however, a tremendous amount of research in
the field of synthetic organic chemistry has been devoted to methods of producing only one enantiomer of a useful compound and
not the other. This effort probably represents the single biggest aim of synthetic organic chemistry through the last quarter century.
Enantiomers may have very different biological properties.
Obtaining enantiomerically pure compounds is very important in medicine and the pharmaceutical industry.

5.12: Chirality in Nature and Chiral Environments is shared under a CC BY-SA 4.0 license and was authored, remixed, and/or curated by Chris
Schaller, Steven Farmer, Dietmar Kennepohl, Layne Morsch, John Roberts, Marjorie C. Caserio, & Marjorie C. Caserio.

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5.S: Stereochemistry at Tetrahedral Centers (Summary)
Concepts & Vocabulary
5.1: Enantiomers and the Tetrahedral Carbon
Every molecule is either chiral (not superimposable on its mirror image) or achiral (superimposable on its mirror image).
Chiral molecules do not have a plane of symmetry, while achiral molecules have one or more planes of symmetry.
Stereoisomers vary by spatial arrangement of atoms but have the same atom connectivity.
Stereoisomers that are mirror images of one another but are not superimposable are called enantiomers.
5.2: The Reason for Handedness in Molecules - Chirality
A Tetrahedral carbon atom bonded to four different substituents is an asymetric carbon (also called a stereocenter or chiral
carbon), which typically leads to a chiral molecule (meso compounds are the exception in section 5.7).
5.3: Optical Activity
Enantiomers cause rotation of plane-polarized light in equal amounts in opposite directions. This is called optical activity.
Clockwise rotation is called dextrorotatory (+) and counter-clockwise is called levorotatory (-).
Specific rotation is the amount that a sample of a chemical rotates planne-polarized light. It can be used to calculate the purity
of a mixture of enantiomers called the enantiomeric excess.
Resolution is the separation of a mixture of enatiomers.
Racemates are defined as a 50:50 mixture of enantiomers, resulting in a sample that is not optically active. The process of
forming a racemic mixture is called racemization.
5.4: Pasteur's Discovery of Enantiomers
5.5: Sequence Rules for Specifying Configuration
Use the CIP rules to determine the priority of each substituent attached to a chiral carbon to determine whether configuration is
R or S. With the lowest priority group facing away from you, draw an arc connecting groups 1-2-3. If that arc is clockwise, the
configuration is R. If counterclockwise, the configuration is S.
5.6: Diastereomers
Stereoisomers that are not mirror images of one another are called diastereomers.
Diastereomers have two or more stereocenters. The configurations of the stereocenters cannot be inverse of each other
(example R,R and S,S) because that defines a pair of enantiomers.
5.7: Meso Compounds
Meso compounds are achiral but have chiral centers. This is caused by having an internal plane of symmetry that allows the
two molecules to be superimposable on one another and be optically inactive.
5.8: Racemic Mixtures and the Resolution of Enantiomers
Each component of a racemic mixture rotates plane polarized light an equal amount in opposite directions, so there is no
optical activity.
Racemic mixtures can be separated into the component enantiomers by reaction with a chiral reagent, which will form
diastereomer intermediates of the molecules which can then be separated. Following separation the chiral reagent is removed
to yield the two pure enantiomers.
5.9: A Review of Isomerism
There are several categories of isomers with the largest distinction between:
constitutional (structural) isomers that contain the same number of each atom but differ in connectivity
stereoisomers that have all the same atoms with the same connectivity, but only differ in how the atoms are arranged three
dimensionally
In addition to the diastereomers and enantiomers that have been discussed at length in this chapter, stereoisomers can also be:
cis/trans or E/Z isomers which differ by spatial arrangement around a double bond
conformational isomers (conformers) which occur due to free rotation of sigma bonds

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5.10: Chirality at Nitrogen, Phosphorus, and Sulfur
Nitrogen when bonded to three different atoms is chiral, however the lone pair of electrons moves freely between positions on
the Nitrogen causing these molecules to become a racemic mixture.
When bonded to four different atoms in quaternary ammonium salts, nitrogen atoms lead to chiral molecules.
Organic phosphates with four different groups can also be chiral.
5.11: Prochirality
When a carbon can be converted to a chiral center by changing only one of its attached groups, it is called prochiral.
If a molecule has two hydrogens on the same atom and replacement of either one with deuterium would lead to enantiomers,
the hydrogens are enantiotopic.
Similarly if this replacement would lead to diastereomer molecules, the hydrogens are diastereotopic.
If replacement of a hydrogen would not lead to a chiral center being created, they are termed homotopic.
5.12: Chirality in Nature and Chiral Environments

Skills to Master

Skill 5.1 Identify stereocenters in molecular structures.

Skill 5.2 Identify whether two structures are identical (not meso), constitutional isomers, enantiomers, diastereomers or meso
and identical.
Skill 5.3 Explain how plane polarized light is used to show optical activity.
Skill 5.4 Calculate specific rotation from experimental data.
Skill 5.5 Calculate optical purity and enantiomeric excess from experimental data.
Skill 5.6 Determine configuration of stereocenters as R or S.
Skill 5.7 Draw the enantiomer and diastereomers of a given compound with one or more stereocenters.
Skill 5.8 Identify planes of symmetry in meso compounds.
Skill 5.9 Describe a process for separating a mixture of enantiomers.
Skill 5.10 Explain why racemic mixtures are optically inactive.
Skill 5.11 Explain the difference between constitutional and stereoisomers.
Skill 5.12 Give an example of a chiral center that is not carbon.

Memorization Tasks
MT 5.1 Memorize the rules for determining R and S configuration.
MT 5.2 Memorize the types of isomers and how to identify them.

5.S: Stereochemistry at Tetrahedral Centers (Summary) is shared under a CC BY-SA 4.0 license and was authored, remixed, and/or curated by
Layne Morsch & Kelly Matthews.

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5.xx: Enantiomers and Diastereomers
 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.

 Exercise 5.xx. 1

When you have one enantiomer that rotates plane polarized light clockwise, why does a racemic mixture of that compound not
rotate plane polarized light?

Answer
Since a racemic mixture consists of equal amounts of both enantiomers, one enantiomer will rotate plane polarized light
clockwise, while the other enantiomer will rotate plane polarized light counterclockwise an equal amount, causing them to
cancel out, and the racemic mixture being not optically active.

5.xx: Enantiomers and Diastereomers is shared under a CC BY-SA 4.0 license and was authored, remixed, and/or curated by Steven Farmer,
Dietmar Kennepohl, Zachary Sharrett, William Reusch, & William Reusch.

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 CHAPTER OVERVIEW
6: An Overview of Organic Reactions
 Learning Objectives

After you have completed Chapter 6, you should be able to

1. fulfill the detailed objectives listed under each individual section.
2. identify the polarity pattern in the common functional groups, and explain the importance of being able to do so.
3. describe the essential differences between polar and radical reactions, and assign a given reaction to one of these two
categories.
4. discuss how kinetic and thermodynamic factors determine the rate and extent of a chemical reaction.
5. use bond dissociation energies to calculate the ΔH° of simple reactions, and vice versa.
6. draw and interpret reaction energy diagrams.
7. define, and use in context, the new key terms.

This chapter is designed to provide a gentle introduction to the subject of reaction mechanisms. Two types of reactions are
introduced—polar reactions and radical reactions. The chapter briefly reviews a number of topics you should be familiar with,
including rates and equilibria, elementary thermodynamics and bond dissociation energies. You must have a working knowledge of
these topics to obtain a thorough understanding of organic reaction mechanisms. Reaction energy diagrams are used to illustrate the
energy changes that take place during chemical reactions, and to emphasize the difference between a reaction intermediate and a
transition state.
6.1: Kinds of Organic Reactions
6.2: How Organic Reactions Occur - Mechanisms
6.3: Radical Reactions
6.4: Polar Reactions
6.5: An Example of a Polar Reaction - Addition of HBr to Ethylene
6.6: Using Curved Arrows in Polar Reaction Mechanisms
6.7: Describing a Reaction - Equilibria, Rates, and Energy Changes
6.8: Describing a Reaction - Bond Dissociation Energies
6.9: Describing a Reaction - Energy Diagrams and Transition States
6.10: Describing a Reaction- Intermediates
6.11: A Comparison between Biological Reactions and Laboratory Reactions
6.S: An Overview of Organic Reactions (Summary)

6: An Overview of Organic Reactions is shared under a CC BY-SA 4.0 license and was authored, remixed, and/or curated by Steven Farmer &
Dietmar Kennepohl.

1
6.1: Kinds of Organic Reactions
 Objective

After completing this section, you should be able to list and describe the four important “kinds” of reactions that occur in
organic chemistry.

 Key Terms

Make certain that you can define, and use in context, the key terms below.
addition reaction
elimination reaction
rearrangement reaction
substitution reaction

 Study Notes
It is sufficient that you know the general form of each kind of reaction. However, given a chemical equation, you should be
able to recognize which kind of reaction it involves.

If you scan any organic textbook you will encounter what appears to be a very large, often intimidating, number of reactions. These
are the "tools" of a chemist, and to use these tools effectively, we must organize them in a sensible manner and look for patterns of
reactivity that permit us make plausible predictions. Most of these reactions occur at special sites of reactivity known as functional
groups, and these constitute one organizational scheme that helps us catalog and remember reactions.

Ultimately, the best way to achieve proficiency in organic chemistry is to understand how
reactions take place, and to recognize the various factors that influence their course.
First, we identify four broad classes of reactions based solely on the structural change occurring in the reactant molecules. This
classification does not require knowledge or speculation concerning reaction paths or mechanisms. The four main reaction classes
are additions, eliminations, substitutions, and rearrangements.
Addition Reaction
R R R R
C C + A B A C C B
R R R R

Elimination Reaction
R R R R
Y C C Z C C + Y Z
R R R R

Substitution Reaction
R R
R C Y + Z R C Z + Y
R R

Rearrangement Reaction
R R R R
R C C X R C C R
R R X R

In an addition reaction the number of σ-bonds in the substrate molecule increases, usually at the expense of one or more π-bonds.
The reverse is true of elimination reactions, i.e.the number of σ-bonds in the substrate decreases, and new π-bonds are often
formed. Substitution reactions, as the name implies, are characterized by replacement of an atom or group (Y) by another atom or
group (Z). Aside from these groups, the number of bonds does not change. A rearrangement reaction generates an isomer, and
again the number of bonds normally does not change.

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The examples illustrated above involve simple alkyl and alkene systems, but these reaction types are general for most functional
groups, including those incorporating carbon-oxygen double bonds and carbon-nitrogen double and triple bonds. Some common
reactions may actually be a combination of reaction types.

 Example 6.1.1: Reaction of an Ester with Ammonia

The reaction of an ester with ammonia to give an amide, as shown below, appears to be a substitution reaction ( Y = CH3O & Z
= NH2 ); however, it is actually two reactions, an addition followed by an elimination.
H
O + NH3 O − CH3OH O
R C R C O R C
addition elimination
O CH3 NH2
NH2 CH3
ester amide

 Example 6.1.2: The Addition of water to a Nitrile

The addition of water to a nitrile does not seem to fit any of the above reaction types, but it is simply a slow addition reaction
followed by a rapid rearrangement, as shown in the following equation. Rapid rearrangements of this kind are called
tautomerizations.
H
+ H 2O N H fast N H
R C N R C R C
addition rearrangement
O H O
nitrile amide

Exercises
Questions
Q6.1.1
Classify each reaction as addition, elimination, substitution, or rearrangement.

Solutions
S6.1.1
A = Substitution; B = Elimination; C = Addition

6.1: Kinds of Organic Reactions is shared under a CC BY-SA 4.0 license and was authored, remixed, and/or curated by Steven Farmer, Dietmar
Kennepohl, Krista Cunningham, William Reusch, & William Reusch.

6.1.2 https://chem.libretexts.org/@go/page/31436
6.2: How Organic Reactions Occur - Mechanisms
 Objectives

After completing this section, you should be able to

1. explain the difference between heterolytic and homolytic bond breakage, and between heterogenic and homogenic bond
formation.
2. state the two reaction types involved in symmetrical and unsymmetrical processes.

 Key Terms
Make certain that you can define, and use in context, the key terms below.
heterogenic
heterolytic
homogenic
homolytic
polar reaction
radical reaction
reaction mechanism

 Study Notes

Upon first reading first four key terms, it is easy to be puzzled. The ending of the word tells you whether a bond is being
formed (‑genic) or broken (‑lytic), while the root of the word describes the nature of that formation or decomposition. So
hetero (meaning different) reactions involve asymmetrical bond making (or breaking) and homo (meaning same) involve
symmetrical processes.
Because one pair of electrons constitutes a single bond, the unsymmetrical making or breaking of that bond in a hetero
processes are described as polar reactions. Similarly, symmetrical homo processes of bond making and breaking are called
radical reactions. Radicals (sometimes referred to as free radicals) are highly reactive neutral chemical species with one
unpaired electron. In later sections we discuss radical and polar reactions in more detail.

The Arrow Notation in Mechanisms

Since chemical reactions involve the breaking and making of bonds, a consideration of the movement of bonding (and non-
bonding) valence shell electrons is essential to this understanding. It is now common practice to show the movement of electrons
with curved arrows, and a sequence of equations depicting the consequences of such electron shifts is termed a mechanism. In
general, two kinds of curved arrows are used in drawing mechanisms:

A full head on the arrow indicates the A B A + B

movement or shift of an electron pair: both electrons
transfer to B

A partial head (fishhook) on the arrow A B A + B

indicates the shift of a single electron: one electron goes to A;
the other electron to B

The use of these symbols in bond-breaking and bond-making reactions is illustrated below. If a covalent single bond is broken so
that one electron of the shared pair remains with each fragment, as in the first example, this bond-breaking is called homolysis. If
the bond breaks with both electrons of the shared pair remaining with one fragment, as in the second and third examples, this is
called heterolysis.

Bond-Breaking Bond-Making

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 R R R R
homolysis
R C Y R C + Y R C + Y R C Y
R R R R

R R R R
heterolysis
R C Y R C + Y R C + Y R C Y
R R R R

R R R R
heterolysis
R C Y R C + Y R C + Y R C Y
R R R R

Other Arrow Symbols

Chemists also use arrow symbols for other purposes, and it is essential to use them correctly.

The Reaction Arrow The Equilibrium Arrow The Resonance Arrow

The following equations illustrate the proper use of these symbols:

CH4 + 2O2 CO2 + H 2O + energy

O O
H 3C C + H 2O H 3C C + H 3O
O H O

H H
H2 C C CH2 H2C C CH2

Reactive Intermediates
The products of bond breaking, shown above, are not stable in the usual sense, and cannot be isolated for prolonged study. Such
species are referred to as reactive intermediates, and are believed to be transient intermediates in many reactions. The general
structures and names of four such intermediates are given below.

Charged Intermediates Uncharged Intermediates

R R
R C R C
R R

a carbocation a radical
R R
R C C
R R

a carbanion a carbene

A pair of widely used terms, related to the Lewis acid-base notation, should also be introduced here.
Electrophile: An electron deficient atom, ion or molecule that has an affinity for an electron pair, and will bond to a base or
nucleophile.
Nucleophile: An atom, ion or molecule that has an electron pair that may be donated in bonding to an electrophile (or Lewis
acid).
Using these definitions, it is clear that carbocations ( called carbonium ions in the older literature ) are electrophiles and carbanions
are nucleophiles. Carbenes have only a valence shell sextet of electrons and are therefore electron deficient. In this sense they are
electrophiles, but the non-bonding electron pair also gives carbenes nucleophilic character. As a rule, the electrophilic character
dominates carbene reactivity. Carbon radicals have only seven valence electrons, and may be considered electron deficient;
however, they do not in general bond to nucleophilic electron pairs, so their chemistry exhibits unique differences from that of
conventional electrophiles. Radical intermediates are often called free radicals.

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The importance of electrophile / nucleophile terminology comes from the fact that many organic reactions involve at some stage
the bonding of a nucleophile to an electrophile, a process that generally leads to a stable intermediate or product. Reactions of this
kind are sometimes called ionic reactions, since ionic reactants or products are often involved. Some common examples of ionic
reactions and their mechanisms may be examined below.
The shapes ideally assumed by these intermediates becomes important when considering the stereochemistry of reactions in which
they play a role. A simple tetravalent compound like methane, CH4, has a tetrahedral configuration. Carbocations have only three
bonds to the charge bearing carbon, so it adopts a planar trigonal configuration. Carbanions are pyramidal in shape ( tetrahedral if
the electron pair is viewed as a substituent), but these species invert rapidly at room temperature, passing through a higher energy
planar form in which the electron pair occupies a p-orbital. Radicals are intermediate in configuration, the energy difference
between pyramidal and planar forms being very small. Since three points determine a plane, the shape of carbenes must be planar;
however, the valence electron distribution varies.

Ionic Reactions
The principles and terms introduced in the previous sections can now be summarized and illustrated by the following three
examples. Reactions such as these are called ionic or polar reactions, because they often involve charged species and the bonding
together of electrophiles and nucleophiles. Ionic reactions normally take place in liquid solutions, where solvent molecules assist
the formation of charged intermediates.
CH3 CH3
H 3C C O + H Cl H 3C C Cl + H2O
CH3 H CH3 The substitution reaction shown on the left can be viewed as taking
place in three steps. The first is an acid-base equilibrium, in which HCl
protonates the oxygen atom of the alcohol. The resulting conjugate acid
then loses water in a second step to give a carbocation intermediate.
CH3 H CH3
H 3C C O Cl H 3C C Cl +
Finally, this electrophile combines with the chloride anion nucleophile
H 2O
CH3 H CH3 to give the final product.
conjugate conjugate electrophile nucleophile
acid base

H H
H H
C C + H Br H C C Br
H H H H The addition reaction shown on the left can be viewed as taking place in
two steps. The first step can again be considered an acid-base
equilibrium, with the pi-electrons of the carbon-carbon double bond
H H functioning as a base. The resulting conjugate acid is a carbocation, and
H C C Br
H
this electrophile combines with the nucleophilic bromide anion.
H
electrophile nucleophile

CH3 H CH3
H 3C C Cl + KOH C C + H 2O + KCl
H CH3
The elimination reaction shown on the left takes place in one step. The
CH3
bond breaking and making operations that take place in this step are
described by the curved arrows. The initial stage may also be viewed as
H CH3 H CH3 an acid-base interaction, with hydroxide ion serving as the base and a
+ H 2O + KCl
H C C Cl + K OH C C hydrogen atom component of the alkyl chloride as an acid.
H CH3 H CH3

6.2.3 https://chem.libretexts.org/@go/page/31437
 rearrangement (tautomerism)

H There are many kinds of molecular rearrangements. The examples

H O O
C C shown on the left are from an important class called tautomerization
C C
R R or, more specifically, keto-enol tautomerization. Tautomers are rapidly
keto
tautomer
enol
tautomer interconverted constitutional isomers, usually distinguished by a
different bonding location for a labile hydrogen atom (colored red here)
H and a differently located double bond. The equilibrium between
H N R N R
C C tautomers is not only rapid under normal conditions, but it often
C C
R R strongly favors one of the isomers (acetone, for example, is 99.999%
imine enamine
tautomer tautomer keto tautomer). Even in such one-sided equilibria, evidence for the
presence of the minor tautomer comes from the chemical behavior of
H O
H the compound. Tautomeric equilibria are catalyzed by traces of acids or
O
C N
C N
bases that are generally present in most chemical samples.
nitroso oxime
tautomer tautomer

6.2: How Organic Reactions Occur - Mechanisms is shared under a CC BY-SA 4.0 license and was authored, remixed, and/or curated by Steven
Farmer, Dietmar Kennepohl, Krista Cunningham, William Reusch, & William Reusch.

6.2.4 https://chem.libretexts.org/@go/page/31437
6.3: Radical Reactions
 Objectives

After completing this section, you should be able to

1. give an example of a radical substitution reaction.
2. identify the three steps (initiation, propagation and termination) that occur in a typical radical substitution reaction.
3. write out the steps involved in a simple radical substitution reaction, such as the chlorination of methane.
4. explain why the halogenation of an alkane is not a particularly useful method of preparing specific alkyl halides.

 Key Terms
Make certain that you can define, and use in context, the key terms below.
chain reaction
initiation step
propagation step
radical substitution
termination step

 Study Notes

A radical substitution reaction is a reaction which occurs by a free radical mechanism and results in the substitution of one or
more of the atoms or groups present in the substrate by different atoms or groups.
The initiation step in a radical chain reaction is the step in which a free radical is first produced. A termination step of a radical
chain reaction is one in which two radicals react together in some way so that the chain can no longer be propagated.
While radical halogenation of very simple alkanes can be an effective synthetic strategy, it cannot be employed for larger more
complex alkanes to yield specific alkyl halides, since the reactive nature of radicals always leads to mixtures of single- and
multiple-halogenated products.

The Three Phases of Radical Chain Reactions

Because of their high reactivity, free radicals have the potential to be both extremely powerful chemical tools and extremely
harmful contaminants. Much of the power of free radical species stems from the natural tendency of radical processes to occur in a
chain reaction fashion. Radical chain reactions have three distinct phases: initiation, propagation, and termination.
Initiation:
(heat or light)
A B A + B

Propagation:

A + C D A C + D

D + E F D E + F etc.
Termination:

F + G F G

The initiation phase describes the step that initially creates a radical species. In most cases, this is a homolytic cleavage event, and
takes place very rarely due to the high energy barriers involved. Often the influence of heat, UV radiation, or a metal-containing
catalyst is necessary to overcome the energy barrier.
Molecular chlorine and bromine will both undergo homolytic cleavage to form radicals when subjected to heat or light. Other
functional groups which also tend to form radicals when exposed to heat or light are chlorofluorocarbons, peroxides, and the
halogenated amide N-bromosuccinimide (NBS).

6.3.1 https://chem.libretexts.org/@go/page/31438
 (heat or light) (heat or light)
Cl Cl 2 Cl R O O R 2 OR

O O

(heat or light)
N Br N + Br

O O
N-bromosuccinimide
(NBS)

The propagation phase describes the 'chain' part of chain reactions. Once a reactive free radical is generated, it can react with
stable molecules to form new free radicals. These new free radicals go on to generate yet more free radicals, and so on. Propagation
steps often involve hydrogen abstraction or addition of the radical to double bonds.
R R
X + C R X H + C
H R RR

X
R R R
X + C C C C
R R RR R

Chain termination occurs when two free radical species react with each other to form a stable, non-radical adduct. Although this
is a very thermodynamically downhill event, it is also very rare due to the low concentration of radical species and the small
likelihood of two radicals colliding with one another. In other words, the Gibbs free energy barrier is very high for this reaction,
mostly due to entropic rather than enthalpic considerations. The active sites of enzymes, of course, can evolve to overcome this
entropic barrier by positioning two radical intermediates adjacent to one another.

H3 C + Cl H3C Cl

Exercises
Questions
Q6.3.1
Radical chlorination of alkanes are not useful due to uncontrolled substitution. Draw the mono-substituted products of Cl2 reacting
with 2-methylbutane.
Q6.3.2
Propose a radical mechanism for the following reaction:

Solutions
S6.3.1

6.3.2 https://chem.libretexts.org/@go/page/31438
S6.3.2

6.3: Radical Reactions is shared under a CC BY-SA 4.0 license and was authored, remixed, and/or curated by Steven Farmer, Dietmar Kennepohl,
Krista Cunningham, Tim Soderberg, & Tim Soderberg.

6.3.3 https://chem.libretexts.org/@go/page/31438
6.4: Polar Reactions
 Objectives

After completing this section, you should be able to

1. identify the positive and negative ends of the bonds present in the common functional groups.
2. explain how bond polarity can be enhanced by the interaction of a functional group with a solvent, metal cation or acid.
3. explain how the polarizability of an atom can be an important factor in determining the reactivity of a bond.
4. describe the heterolytic bond-breaking process.
5. use curved (curly) arrows to indicate the movement of electron pairs during bond breakage and bond formation.
6. predict whether a given species (compound or ion) is likely to behave as a nucleophile or as an electrophile.

 Key Terms
Make certain that you can define, and use in context, the key terms below.
electrophile
nucleophile
polar reaction
polarizability

 Study Notes

You may wish to review Section 2.1 before you begin this section. The relative electronegativities of the elements shown in the
periodic table should already be familiar. Remember that it is the relative electronegativities that are important, not the actual
numerical values.
Make sure that you understand the polarity patterns of the common functional groups. Do not try to memorize these polarities;
rather, concentrate on why they arise. You will encounter these group polarities so frequently that they will soon become
“second nature” to you.

Halogens and the Character of the Carbon-Halogen Bond

With respect to electronegativity, most halogens are more electronegative than carbon. This results in a carbon-halogen bond that is
polarized. As shown in the image below, the carbon atom has a partial positive charge, while the halogen has a partial negative
charge.
𝛅+ 𝛅−
C X

The following table shows the relationship between the halogens and electronegativity. Notice, as we move up the periodic table
from iodine to fluorine, electronegativity increases.

Electronegativity I < Br < Cl < F

The following table shows the relationships between bond length, bond strength, and molecular size. As we progress down the
periodic table from fluorine to iodine, molecular size increases. As a result, we also see an increase in bond length. Conversely, as
molecular size increases and we get longer bonds, the strength of those bonds decreases.

Bond length C–F < C–Cl < C–Br < C–I

Bond strength C–I < C–Br < C–Cl < C–F

Molecular size F < Cl < Br < I

6.4.1 https://chem.libretexts.org/@go/page/31439
The influence of bond polarity
Of the four halogens, fluorine is the most electronegative and iodine the least. That means that the electron pair in the carbon-
fluorine bond will be dragged most towards the halogen end. Looking at the methyl halides as simple examples:
H H H H
𝛅+ 𝛅− 𝛅+ 𝛅− 𝛅+ 𝛅− 𝛅+ 𝛅−

C F C Cl C Br C I
H H H H
H H H H

The electronegativities of carbon and iodine are not very different, and so there will be little separation of charge on the bond. One
of the important set of reactions of alkyl halides involves replacing the halogen by something else - substitution reactions. These
reactions can involve the carbon-halogen bond breaking to give positive and negative ions. The ion with the positively charged
carbon atom then reacts with something either fully or slightly negatively charged. Alternatively, something either fully or
negatively charged is attracted to the slightly positive carbon atom and pushes off the halogen atom.
You might have thought that either of these would be more effective in the case of the carbon-fluorine bond with the quite large
amounts of positive and negative charge already present. But that's not so - quite the opposite is true! The thing that governs the
reactivity is the strength of the bonds which have to be broken. It is difficult to break a carbon-fluorine bond, but easy to break a
carbon-iodine one.

The Carbonyl Group

C=O is prone to additions and nucleophillic attack because or carbon's positive charge and oxygen's negative charge. The
resonance of the carbon partial positive charge allows the negative charge on the nucleophile to attack the Carbonyl group and
become a part of the structure and a positive charge (usually a proton hydrogen) attacks the oxygen. Just a reminder, the
nucleophile is a good acid therefore "likes protons" so it will attack the side with a positive charge.
Before we consider in detail the reactivity of aldehydes and ketones, we need to look back and remind ourselves of what the
bonding picture looks like in a carbonyl. Carbonyl carbons are sp2 hybridized, with the three sp2 orbitals forming overlaps with
orbitals on the oxygen and on the two carbon or hydrogen atoms. These three bonds adopt trigonal planar geometry. The remaining
unhybridized 2p orbital on the central carbonyl carbon is perpendicular to this plane, and forms a ‘side-by-side’ pi bond with a 2p
orbital on the oxygen.

R
C O
R

The carbon-oxygen double bond is polar: oxygen is more electronegative than carbon, so electron density is higher on the oxygen
side of the bond and lower on the carbon side. Recall that bond polarity can be depicted with a dipole arrow, or by showing the
oxygen as holding a partial negative charge and the carbonyl carbon a partial positive charge.

O O 𝛅− O O
C C 𝛅+ C C
R R R R R R R R
minor

A third way to illustrate the carbon-oxygen dipole is to consider the two main resonance contributors of a carbonyl group: the
major form, which is what you typically see drawn in Lewis structures, and a minor but very important contributor in which both
electrons in the pbond are localized on the oxygen, giving it a full negative charge. The latter depiction shows the carbon with an
empty 2p orbital and a full positive charge.

Some Carbonyl Compounds

formaldehy carboxylic acid
Compound aldehyde ketone ester amide enone acyl halide
de acid anhydride
O O R’’
O O O O O O O O
Structure C C C
R
C
OH R
C
OR’ R
C
N
R’’
R
C
C
C
R''' R
C
X R
C
O
C
R'
R H R R’ H H
R’ R’

General RC(O)C(R')
RCHO RCOR' CH2O RCOOH RCOOR' RCONR'R'' RCOX RCO2COR'
Formula CR''R'''

6.4.2 https://chem.libretexts.org/@go/page/31439
Nucleophilic Addition to Aldehydes and Ketones
The result of carbonyl bond polarization, however it is depicted, is straightforward to predict. The carbon, because it is electron-
poor, is an electrophile: it is a great target for attack by an electron-rich nucleophilic group. Because the oxygen end of the carbonyl
double bond bears a partial negative charge, anything that can help to stabilize this charge by accepting some of the electron
density will increase the bond’s polarity and make the carbon more electrophilic. Very often a general acid group serves this
purpose, donating a proton to the carbonyl oxygen.

H A Mg2+
O O
C C
R R R R

The same effect can also be achieved if a Lewis acid, such as a magnesium ion, is located near the carbonyl oxygen. Unlike the
situation in a nucleophilic substitution reaction, when a nucleophile attacks an aldehyde or ketone carbon there is no leaving group
– the incoming nucleophile simply ‘pushes’ the electrons in the pi bond up to the oxygen.

O O
C R C
R R R
Nu

Nu

Alternatively, if you start with the minor resonance contributor, you can picture this as an attack by a nucleophile on a carbocation.

O O
C R C
R R R
Nu

Nu

After the carbonyl is attacked by the nucleophile, the negatively charged oxygen has the capacity to act as a nucleophile. However,
most commonly the oxygen acts instead as a base, abstracting a proton from a nearby acid group in the solvent or enzyme active
site.

H A

O OH
R C R C
Nu R Nu R

This very common type of reaction is called a nucleophilic addition. In many biologically relevant examples of nucleophilic
addition to carbonyls, the nucleophile is an alcohol oxygen or an amine nitrogen, or occasionally a thiol sulfur. In one very
important reaction type known as an aldol reaction, the nucleophile attacking the carbonyl is a resonance-stabilized carbanion. In
this chapter, we will concentrate on reactions where the nucleophile is an oxygen or nitrogen.
1. Nucleophilic Addition to Aldehydes and Ketones
2. Nucleophilic Substitution of RCOZ (Z = Leaving Group)
3. General reaction
4. General mechanism

Polarity Patterns in Other Common Functional Groups

𝛅− 𝛅−
R 𝛅+ OH R NH
𝛅− 2
R 𝛅+ SH
C C𝛅+ C
R R R
R R R

𝛅+ 𝛅+
R 𝛅− MgBr R 𝛅− Li
C C
R R
R R

R R
𝛅+ 𝛅−
R C N C C
R R

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Nucleophile?
Nucleophilic functional groups are those which have electron-rich atoms able to donate a pair of electrons to form a new covalent
bond. In both laboratory and biological organic chemistry, the most relevant nucleophilic atoms are oxygen, nitrogen, and sulfur,
and the most common nucleophilic functional groups are water, alcohols, phenols, amines, thiols, and occasionally carboxylates.
More specifically in laboratory reactions, halide and azide (N3-) anions are commonly seen acting as nucleophiles.
Of course, carbons can also be nucleophiles - otherwise how could new carbon-carbon bonds be formed in the synthesis of large
organic molecules like DNA or fatty acids? Enolate ions (section 7.5) are the most common carbon nucleophiles in biochemical
reactions, while the cyanide ion (CN-) is just one example of a carbon nucleophile commonly used in the laboratory. Reactions with
carbon nucleophiles will be dealt with in chapters 13 and 14, however - in this chapter and the next, we will concentrate on non-
carbon nucleophiles.
When thinking about nucleophiles, the first thing to recognize is that, for the most part, the same quality of 'electron-richness' that
makes a something nucleophilic also makes it basic: nucleophiles can be bases, and bases can be nucleophiles. It should not be
surprising, then, that most of the trends in basicity that we have already discussed also apply to nucleophilicity.

Neutral Nucleophiles Charged Nucleophiles

⊝OH, ⊝OR, ⊝NH , ⊝NHR, ⊝NR , ⊝SH, ⊝SR, ⊝SeR, ⊝Cl, ⊝Br, ⊝I, ⊝F,
2 2
H2O, NH3, RNH2, R2NH, R3N, ROH, RCOOH, RSH, and PR3 ⊝CN, RCOO⊝

Electrophiles
In the vast majority of the nucleophilic substitution reactions you will see in this and other organic chemistry texts, the electrophilic
atom is a carbon which is bonded to an electronegative atom, usually oxygen, nitrogen, sulfur, or a halogen. The concept of
electrophilicity is relatively simple: an electron-poor atom is an attractive target for something that is electron-rich, i.e. a
nucleophile. However, we must also consider the effect of steric hindrance on electrophilicity. In addition, we must discuss how the
nature of the electrophilic carbon, and more specifically the stability of a potential carbocationic intermediate, influences the SN1
vs. SN2 character of a nucleophilic substitution reaction. Edit section
Consider two hypothetical SN2 reactions: one in which the electrophile is a methyl carbon and another in which it is tertiary carbon.

Nu X Nu X

CH3 H

H3 C X H
H3 C H X

Because the three substituents on the methyl carbon electrophile are tiny hydrogens, the nucleophile has a relatively clear path for
backside attack. However, backside attack on the tertiary carbon is blocked by the bulkier methyl groups. Once again, steric
hindrance - this time caused by bulky groups attached to the electrophile rather than to the nucleophile - hinders the progress of an
associative nucleophilic (SN2) displacement.
The factors discussed in the above paragraph, however, do not prevent a sterically-hindered carbon from being a good electrophile -
they only make it less likely to be attacked in a concerted SN2 reaction. Nucleophilic substitution reactions in which the
electrophilic carbon is sterically hindered are more likely to occur by a two-step, dissociative (SN1) mechanism. This makes perfect
sense from a geometric point of view: the limitations imposed by sterics are significant mainly in an SN2 displacement, when the
electrophile being attacked is a sp3-hybridized tetrahedral carbon with its relatively ‘tight’ angles of 109.4o. Remember that in an
SN1 mechanism, the nucleophile attacks an sp2-hybridized carbocation intermediate, which has trigonal planar geometry with
‘open’ 120 angles.

CH3

Nu
H 3C CH3

6.4.4 https://chem.libretexts.org/@go/page/31439
With this open geometry, the empty p orbital of the electrophilic carbocation is no longer significantly shielded from the
approaching nucleophile by the bulky alkyl groups. A carbocation is a very potent electrophile, and the nucleophilic step occurs
very rapidly compared to the first (ionization) step.

Exercises
Questions
Q6.4.1
Label the following either an electrophile or a nucleophile.

Solutions
S6.4.1
A = Electrophile
B = Nucleophile
C = Both (carbonyl carbon is electrophile and oxygen is nucleophile)

6.4: Polar Reactions is shared under a CC BY-SA 4.0 license and was authored, remixed, and/or curated by Steven Farmer, Dietmar Kennepohl,
Krista Cunningham, Tim Soderberg, William Reusch, & William Reusch.

6.4.5 https://chem.libretexts.org/@go/page/31439
6.5: An Example of a Polar Reaction - Addition of HBr to Ethylene
 Objectives

After completing this section, you should be able to

1. give an example of a simple polar reaction (e.g., a electrophilic addition).
2. identify the electrophile and nucleophile in a simple polar reaction.

 Key Terms
Make certain that you can define, and use in context, the key terms below.
electrophilic addition
carbocation

 Study Notes

The curved arrows introduced in this section are used throughout the course to indicate the movement of electron pairs. It takes
practice for the beginning student to feel comfortable using these arrows. Remember that the head of the arrow indicates where
the electron pair moves to; its tail shows where the electron pair comes from. (Chemists often refer to the use of curved arrows
as “electron pushing.")

This page looks at the reaction of the carbon-carbon double bond in alkenes such as ethene with hydrogen halides such as hydrogen
chloride and hydrogen bromide. Symmetrical alkenes (like ethene or but-2-ene) are dealt with first. These are alkenes where
identical groups are attached to each end of the carbon-carbon double bond.

Addition to symmetrical alkenes

All alkenes undergo addition reactions with the hydrogen halides. A hydrogen atom joins to one of the carbon atoms originally in
the double bond, and a halogen atom to the other. For example, with ethene and hydrogen chloride, you get chloroethane:
H2 C CH2 + HCl H3 C CH2Cl

With but-2-ene you get 2-chlorobutane:

H H
H3 C C C CH3 + HCl H3C CH2 C CH3
H
Cl

What happens if you add the hydrogen to the carbon atom at the right-hand end of the double bond, and the chlorine to the left-
hand end? You would still have the same product. The chlorine would be on a carbon atom next to the end of the chain - you would
simply have drawn the molecule flipped over in space. That would be different of the alkene was unsymmetrical - that's why we
have to look at them separately.

Mechanism
The addition of hydrogen halides is one of the easiest electrophilic addition reactions because it uses the simplest electrophile: the
proton. Hydrogen halides provide both an electrophile (proton) and a nucleophile (halide). First, the electrophile will attack the
double bond and take up a set of pi electrons, attaching it to the molecule (1). This is basically the reverse of the last step in the E1
reaction (deprotonation step). The resulting molecule will have a single carbon-carbon bond with a positive charge on one of them
(carbocation). The next step is when the nucleophile (halide) bonds to the carbocation, producing a new molecule with both the
original hydrogen and halide attached to the organic reactant (2). The second step will only occur if a good nucleophile is used.
Mechanism of Electrophilic Addition of Hydrogen Halide to Ethene

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 H X X

H H H H H X
C C H C C H C C H
1 - electrophilic 2 - nucleophilic
H H attack H H trapping H H

Mechanism of Electrophilic Addition of Hydrogen Halide to Propene

H X X

H H H H X H
C C C C H H C C H
1 - electrophilic 2 - nucleophilic
H3 C H attack H3 C H trapping H H

All of the halides (HBr, HCl, HI, HF) can participate in this reaction and add on in the same manner. Although different halides do
have different rates of reaction, due to the H-X bond getting weaker as X gets larger (poor overlap of orbitals)s.

Reaction rates
Variation of rates when you change the halogen
Reaction rates increase in the order HF - HCl - HBr - HI. Hydrogen fluoride reacts much more slowly than the other three, and is
normally ignored in talking about these reactions. When the hydrogen halides react with alkenes, the hydrogen-halogen bond has to
be broken. The bond strength falls as you go from HF to HI, and the hydrogen-fluorine bond is particularly strong. Because it is
difficult to break the bond between the hydrogen and the fluorine, the addition of HF is bound to be slow.
Variation of rates when you change the alkene
This applies to unsymmetrical alkenes as well as to symmetrical ones. For simplicity the examples given below are all symmetrical
ones- but they don't have to be. Reaction rates increase as the alkene gets more complicated - in the sense of the number of alkyl
groups (such as methyl groups) attached to the carbon atoms at either end of the double bond.
For example:
H H H CH3 H3C CH3
C C C C C C
H H H3C H H3C CH3

reactivity increases

There are two ways of looking at the reasons for this - both of which need you to know about the mechanism for the reactions.
Alkenes react because the electrons in the pi bond attract things with any degree of positive charge. Anything which increases the
electron density around the double bond will help this. Alkyl groups have a tendency to "push" electrons away from themselves
towards the double bond. The more alkyl groups you have, the more negative the area around the double bonds becomes.
The more negatively charged that region becomes, the more it will attract molecules like hydrogen chloride. The more important
reason, though, lies in the stability of the intermediate ion formed during the reaction. The three examples given above produce
these carbocations (carbonium ions) at the half-way stage of the reaction:
H H H H
C C H C C
H H H H
a primary carbocation

H CH3 H CH3 ions getting

C C H C C more
energetically
H3C H H3C H stable and so
a secondary carbocation easier to form

H3C CH3 H CH3

C C H3C C C
H3C CH3 H3C CH3
a tertiary carbocation

The stability of the intermediate ions governs the activation energy for the reaction. As you go towards the more complicated
alkenes, the activation energy for the reaction falls. That means that the reactions become faster.

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Addition to unsymmetrical alkenes
In terms of reaction conditions and the factors affecting the rates of the reaction, there is no difference whatsoever between these
alkenes and the symmetrical ones described above. The problem comes with the orientation of the addition - in other words, which
way around the hydrogen and the halogen add across the double bond.
Orientation of addition
If HCl adds to an unsymmetrical alkene like propene, there are two possible ways it could add. However, in practice, there is only
one major product.
H3 C CH2 CH2 Cl
HCl
1-chloropropane
H3C C CH2
H
HCl
H3C CH CH3
Cl
2-chloropropane
MAJOR PRODUCT

This is in line with Markovnikov's Rule which says:

When a compound HX is added to an unsymmetrical alkene, the hydrogen becomes attached to the carbon with the most
hydrogens attached to it already.

In this case, the hydrogen becomes attached to the CH2 group, because the CH2 group has more hydrogens than the CH group.
Notice that only the hydrogens directly attached to the carbon atoms at either end of the double bond count. The ones in the CH3
group are totally irrelevant.

Exercises
1. Supply the missing curved arrows in the equations given below.
a.

b.

c.
Answers:
1. a.

b.

c.

Questions
Q6.5.1
Predict the product of the following reactions:

6.5.3 https://chem.libretexts.org/@go/page/31440
Solutions
S6.5.1

6.5: An Example of a Polar Reaction - Addition of HBr to Ethylene is shared under a CC BY-SA 4.0 license and was authored, remixed, and/or
curated by Jim Clark, Steven Farmer, Dietmar Kennepohl, Krista Cunningham, Tim Soderberg, William Reusch, John Roberts, Marjorie C.
Caserio, & Marjorie C. Caserio.

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6.6: Using Curved Arrows in Polar Reaction Mechanisms
 Objective

After completing this section, you should be able to use curved (curly) arrows, in conjunction with a chemical equation, to
show the movement of electron pairs in a simple polar reaction, such as electrophilic addition.

 Key Terms

Make certain that you can define, and use in context, the key terms below.
electrophlic
nucleophlic

Pushing Electrons and Curved Arrows

Understanding the location of electrons and being able to draw the curved arrows that depict the mechanisms by which
the reactions occur is one of the most critical tools for learning organic chemistry since they allow you to understand
what controls reactions, and how reactions proceed.
Before you can do this you need to understand that a bond is due to a pair of electrons shared between atoms.
When asked to draw a mechanism, curved arrows should be used to show all the bonding changes that occur.
A few simple lessons that illustrate these concepts can be found below.

Lesson 1
If we remove the pair of electrons in a bond, then we BREAK that bond. This is true for single and multiple bonds as shown below:
CH3 CH3
H 3C arrow illustrating electron
C C + Br
H 3C Br flow in a reaction
H 3C CH3

O O arrow illustrating electron

C C flow in resonance
H H H H

arrow illustrating electron

H C N H C N
flow in resonance

Notice that since the starting materials were neutral, the products are also neutral. In general terms, the sum of the charges on the
starting materials MUST equal the sum of the charges on the products since we have the same number of electrons.
The first example is a REACTION since we broke a sigma bond. In the second two examples, we moved pi electrons into long
pairs. This is RESONANCE.
If we move electrons between two atoms, then we MAKE a new bond:
CH3 CH3
H3C arrow illustrating electron
C C + Br
H3C Br flow in a reaction
H3C CH3

O O arrow illustrating electron

C C flow in resonance
H H H H

arrow illustrating electron

H C N H C N
flow in resonance

We always show electrons moving from electron rich to electron poor.

6.6.1 https://chem.libretexts.org/@go/page/31441
Lesson 2
H
O + H Cl + Cl
H H O
H H

This is a simple acid/base reaction, showing the formation of the hydronium ion produced when hydrochloric acid is dissolved in
water. It is useful to analyze the bond changes that are occurring. Water is functioning as a base and hydrochloric acid as an acid.
Consider the differences in bonding between the starting materials and the products:
electrons are used to
form a new bond to H
new bond
H
O + H Cl + Cl
H H O
H H

bond is broken; lone pair gained from

electrons become a lone breaking H-Cl bond
pair on Cl

One of the lone pairs on the oxygen atom of water was used to form a bond to a hydrogen atom, creating the hydronium ion (H3O+)
seen in the products. The hydrogen-chlorine bond of HCl was broken, and the electrons in this bond became a lone pair on the
chlorine atom, thus generating a chloride ion. We can illustrate these changes in bonding using the curved arrows shown below.

H
O + H Cl + Cl
H H O
H H

Note that in this diagram, the overall charge of the reactants is the same as the overall charge of the products. We can also show the
curved arrows for the reverse reaction:

H
Cl + H Cl + O
O H H
H H

This shows the formation of the new H-Cl bond by using a lone pair of electrons from the electron-rich chloride ion to form a bond
to an electron poor hydrogen atom of the hydronium ion. Because hydrogen can only form one bond, the oxygen-hydrogen bond is
broken and its electrons become a lone pair on the electron-poor oxygen atom. Notice that the charges balance!

Lesson 3
In this section, we will look at the curved arrows for some nucleophilic substitution reactions. Overall, the processes involved are
similar to those for the acid/base reactions described above. In a nucleophilic substitution reaction, an electron-rich nucleophile
(Nu) becomes bonded to an electron-poor carbon atom, and a leaving group (LG) is displaced. In bonding terms, we must make a
Nu-C bond and break a C-LG bond.
R R
Nu + R R +
C C LG
R LG R Nu

Let's consider the stepwise SN1 reaction between (1-chloroethyl)benzene and sodium cyanide. The first step of this process is
breaking the C-Cl bond, where the electrons in that bond become a lone pair on the chlorine atom. The carbon atom has lost
electrons and therefore becomes positive, generating a secondary carbocation. Because the chlorine atom gained an additional lone
pair of electrons, it becomes a negatively charged chloride ion.

Cl + Cl

(1-chloroethyl)benzene

In the second step, the electron-rich nucleophile donates electrons to form a new C-C bond with the electron-poor secondary
carbocation.

+ C +
Na C N N Na

In an SN2 reaction, the bond forming and breaking processes occur simultaneously. The scheme below shows the Nu donating
electrons to form a new C-C bond at the same time that the C-Cl bond is breaking. The electrons in the C-Cl bond become a long

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pair on the chlorine atom, generating a chloride ion. Forming and breaking the bonds simultaneously allows carbon to obey the
octet rule throughout this process.

Cl + C + Na Cl
Na C N N

Notice that in all steps for the processes above, the overall charges of the starting materials match those of the products.

Lesson 4
This section will dissect another substitution reaction, although it is more involved. Let's consider the SN1 reaction of tert-butyl
bromide with water.

+ O + H Br
Br H H OH

It can be helpful to take inventory of which bonds have been formed, and which bonds have been broken.
FORMED: C-O, H-Br
+ O + H Br
Br H H OH BROKEN: C-Br, O-H

The curved arrows we draw must account for ALL of these bonding changes. Since we are dealing with an SN1 reaction process,
the first step will be cleavage of the C-Br bond to give a carbocation and and a bromide anion.

+ Br
Br

Water then acts as a nucleophile, using one of its lone pairs to form a bond to the electron-poor t-butyl cation. This generates an
oxonium ion, where oxygen has three bonds and a positive formal charge.

O H
+ O
H H
H

The final step is an acid/base reaction between the bromide anion generated in step 1 and the oxonium product of step 2. The
bromide anion acts as a base, using a lone pair to form a bond to one of the hydrogen atoms. The O-H bond then breaks, and its
electrons become a lone pair on oxygen. This gives the final products of HBr and t-butyl alcohol.

H
O + Br + H Br
OH
H

Notice that in each of the mechanistic steps above, the overall charge of the reactant side balances with the overall charge of the
product side.
While the above process was broken down into distinct steps, however it is important to note that mechanisms are almost always
shown as a continuous process. The overall mechanism for this processes can be found below:

+ O
Br H H

+ H Br
OH H
O + Br
H

Now consider the reverse reaction, i.e. the reaction of t-butyl alcohol with hydrobromic acid to generate t-butyl bromide and water.
The scheme is shown below, along with an analysis of the bonds formed and broken in this process:
FORMED: C-Br, O-H
+ H Br + O
OH Br H H BROKEN: C-O, H-Br

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The mechanism must occur via the same pathway as shown above (Law of Macroscopic Reversibility), however this mechanism
can still be deduced without knowing that. First, it is known that HBr is a strong acid and can donate a proton to a base. The most
basic sites in the whole system are the lone pairs on the oxygen atom of t-butanol. Since the lone pairs are the electron-rich area of
the molecule, the arrow starts at a lone pair and ends at the proton of HBr. The H-Br bond breaks, pushing its electrons onto the
bromine atom and generating a bromide ion.

H
+ H Br O + Br
OH
H

H O
O +
H H
H

The bromide ion generated in the first step can then react with the t-butyl cation to generate t-butyl bromide.

+ Br
Br

Once again, the above the overall process is broken down into individual steps, however it is more common to illustrate this as one
overall process:

+ H Br H + Br
OH O
H

+ Br
Br

+ O
H H

Curved Arrow Summary

Curved arrows flow from electron rich to electron poor.
Therefore they start from lone pairs or bonds.
The charges in any particular step should always be balanced.
Remember to obey the rules of valence (eg. octet rule for C,N,O,F etc.)
If electrons are taken out of a bond, then that bond is broken.
If electrons are placed between two atoms then it implies a bond is being made.

Exercises
Draw curved arrows to indicate mechanisms for the following reactions:

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Solutions

6.6: Using Curved Arrows in Polar Reaction Mechanisms is shared under a CC BY-SA 4.0 license and was authored, remixed, and/or curated by
Steven Farmer, Dietmar Kennepohl, Layne Morsch, Krista Cunningham, & Krista Cunningham.

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6.7: Describing a Reaction - Equilibria, Rates, and Energy Changes
 Objectives

After completing this section, you should be able to

1. write the equilibrium constant expression for a given reaction.
2. assess, qualitatively, how far a reaction will proceed in a given direction, given the value of Keq.
3. explain the difference between rate and equilibrium.
4. state the relationship between ΔG° and Keq, and use this relationship to determine the value of either of the two variables,
given the other.
5. state the relationship between Gibbs free-energy, enthalpy and entropy, and use the relationship to calculate any one of ΔG°,
ΔH° and ΔS°, given the other two.
6. make a qualitative assessment of whether ΔS° for a given process is expected to be positive or negative.

 Key Terms
Make certain that you can define, and use in context, the key terms below.
exergonic
endergonic
exothermic
endothermic
enthalpy change (heat of reaction), ΔH°
entropy change, ΔS°
reaction mechanism
standard Gibbs free-energy change, ΔG°

 Study Notes

Throughout this course you will be paying a great deal of attention to the mechanisms of the reactions that you study. Some
students see this as a laborious task of little practical use. However, you will find that a knowledge of reaction mechanisms can
help reduce the number of reactions to memorize, provide a connecting link between apparently unrelated reactions, and enable
someone with a basic knowledge of organic chemistry to deduce how a previously unseen reaction might proceed. The
investigation of reaction mechanisms is a popular research area for organic chemists.

Equilibrium Constant
For the hypothetical chemical reaction:
aA + bB ⇌ cC + dD (6.7.1)

the equilibrium constant is defined as:

c d
[C ] [D]
KC = (6.7.2)
[A]a [B]b

The notation [A] signifies the molar concentration of species A. An alternative expression for the equilibrium constant involves
partial pressures:
c d
P P
C D
KP = (6.7.3)
a b
P P
A B

Note that the expression for the equilibrium constant includes only solutes and gases; pure solids and liquids do not appear in the
expression. For example, the equilibrium expression for the reaction

CaH (s) + 2 H O(g) ⇌ Ca (OH) (s) + 2 H (g) (6.7.4)

2 2 2 2

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is the following:
2
[H2 ]
KC = (6.7.5)
2
[ H2 O]

Observe that the gas-phase species H 2

O and H appear in the expression but the solids CaH and Ca(OH) do not appear.
2 2 2

The equilibrium constant is most readily determined by allowing a reaction to reach equilibrium, measuring the concentrations of
the various solution-phase or gas-phase reactants and products, and substituting these values into the Law of Mass Action.

Free Energy
The interaction between enthalpy and entropy changes in chemical reactions is best observed by studying their influence on the
equilibrium constants of reversible reactions. To this end a new thermodynamic function called Free Energy (or Gibbs Free
Energy), symbol ΔG, is defined as shown in the first equation below. Two things should be apparent from this equation. First, in
cases where the entropy change is small, ΔG ≅ΔH . Second, the importance of ΔS in determining ΔG increases with increasing
temperature.
º º
ΔG = ΔH – T ΔS º (6.7.6)

where the temperature is measured in absolute temperature (K).

The free energy function provides improved insight into the thermodynamic driving forces that influence reactions. A negative
ΔGº is characteristic of an exergonic reaction, one which is thermodynamically favorable and often spontaneous, as is the melting

of ice at 1 ºC. Likewise a positive ΔGº is characteristic of an endergonic reaction, one which requires an input of energy from the
surroundings.
For an example of the relationship of free energy to enthalpy consider the decomposition of cyclobutane to ethene, shown in the
following equation. The standard state for all the compounds is gaseous.

This reaction is endothermic, but the increase in number of molecules from one (reactants) to two (products) results in a large
positive ΔSº.
At 25 ºC (298 K):
ΔGº = 19 kcal/mol – 298(43.6) cal/mole = 19 – 13 kcal/mole = +6 kcal/mole.
Thus, the entropy change opposes the enthalpy change, but is not sufficient to change the sign of the resulting free energy change,
which is endergonic. Indeed, cyclobutane is perfectly stable when kept at room temperature.
Because the entropy contribution increases with temperature, this energetically unfavorable transformation can be made favorable
by raising the temperature. At 200 ºC (473 K),
ΔG º = 19 kcal/mol– 473(43.6) cal/mole (6.7.7)

= 19– 20.6 kcal/mole (6.7.8)

=– 1.6kcal/mole. (6.7.9)

This is now an exergonic reaction, and the thermal cracking of cyclobutane to ethene is known to occur at higher temperatures.
º
ΔG =– RT ln K =– 2.303RT log10 K (6.7.10)

where R = 1.987 cal/ K mole T = temperature in K and K = equilibrium constant

 Note
Equation 6.7.10 is important because it demonstrates the fundamental relationship of ΔGº to the equilibrium constant, K .
Because of the negative logarithmic relationship between these variables, a negative ΔGº generates a K>1, whereas a positive
ΔGº generates a K<1. When ΔGº = 0, K = 1. Furthermore, small changes in ΔGº produce large changes in K. A change of 1.4
kcal/mole in ΔGº changes K by approximately a factor of 10. This interrelationship may be explored with the calculator on the

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 right. Entering free energies outside the range -8 to 8 kcal/mole or equilibrium constants outside the range 10-6 to 900,000 will
trigger an alert, indicating the large imbalance such numbers imply.

Exercises
1. At 155°C, the equilibrium constant, Keq, for the reaction

CH CO H + CH CH OH −
↽⇀
− CH CO CH CH +H O (6.7.11)
3 2 3 2 3 2 2 3 2

has a value of 4.0. Calculate ΔG° for this reaction at 155°C.

2. Acetylene (C2H2) can be converted into benzene (C6H6) according to the equation:

3 H−C≡C−H(g) −
↽⇀
− C H (l) (6.7.12)
6 6

At 25°C, ΔG° for this reaction is −503 kJ and ΔH° is −631 kJ. Determine ΔS° and indicate whether the size of ΔS° agrees with
what you would have predicted simply by looking at the chemical equation.

Answers:
1. The entropy change is negative, as one would expect from looking at the chemical equation, since three moles of reactants yield
one mole of product; that is, the system becomes much more “ordered” as it goes from reactants to products.

Contributors and Attributions

William Reusch, Professor Emeritus (Michigan State U.), Virtual Textbook of Organic Chemistry
Jim Clark (Chemguide.co.uk)

6.7: Describing a Reaction - Equilibria, Rates, and Energy Changes is shared under a CC BY-SA 4.0 license and was authored, remixed, and/or
curated by Steven Farmer & Dietmar Kennepohl.

6.7.3 https://chem.libretexts.org/@go/page/31442
6.8: Describing a Reaction - Bond Dissociation Energies
 Objectives

After completing this section, you should be able to

1. predict the value of ΔH° for a gas-phase reaction, given the necessary bond dissociation energy data.
2. predict the dissociation energy of a particular bond, given ΔH° for a reaction involving the bond and any other necessary
bond dissociation energy data.
3. outline the limitations of using bond dissociation energies to predict whether or not a given reaction will occur.

 Key Terms
Make certain that you can define, and use in context, the key terms below.
bond dissociation energy
solvation

 Study Notes

The idea of calculating the standard enthalpy of a reaction from the appropriate bond dissociation energy data should be
familiar to you from your first-year chemistry course.
Solvation is the interaction between solvent molecules and the ions or molecules dissolved in that solvent.

The homolytic bond dissociation energy is the amount of energy needed to break apart one mole of covalently bonded gases into a
pair of radicals. The SI units used to describe bond energy are kiloJoules per mole of bonds (kJ/Mol). It indicates how strongly the
atoms are bonded to each other.

Introduction
Breaking a covalent bond between two partners, A-B, can occur either heterolytically, where the shared pair of electron goes with
one partner or another
+ −
A−B → A +B : (6.8.1)

or
− +
A−B → A : +B (6.8.2)

or homolytically, where one electron stays with each partner.

∙ ∙
A−B → A +B (6.8.3)

The products of homolytic cleavage are radicals and the energy that is required to break the bond homolytically is called the Bond
Dissociation Energy (BDE) and is a measure of the strength of the bond.

Calculation of the BDE

The BDE for a molecule A-B is calculated as the difference in the enthalpies of formation of the products and reactants for
homolysis
∙ ∙
BDE = Δf H (A ) + Δf H (B ) − Δf H (A − B) (6.8.4)

Officially, the IUPAC definition of bond dissociation energy refers to the energy change that occurs at 0 K, and the symbol is D . o

However, it is commonly referred to as BDE, the bond dissociation energy, and it is generally used, albeit imprecisely,
interchangeably with the bond dissociation enthalpy, which generally refers to the enthalpy change at room temperature (298K).
Although there are technically differences between BDEs at 0 K and 298 K, those difference are not large and generally do not
affect interpretations of chemical processes.

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Bond Breakage/Formation
Bond dissociation energy (or enthalpy) is a state function and consequently does not depend on the path by which it occurs.
Therefore, the specific mechanism in how a bond breaks or is formed does not affect the BDE. Bond dissociation energies are
useful in assessing the energetics of chemical processes. For chemical reactions, combining bond dissociation energies for bonds
formed and bonds broken in a chemical reaction using Hess's Law can be used to estimate reaction enthalpies.

 Example 6.8.1: Chlorination of Methane

Consider the chlorination of methane

C H4 + C l2 → C H3 C l + H C l (6.8.5)

the overall reaction thermochemistry can be calculated exactly by combining the BDEs for the bonds broken and bonds formed
CH4 → CH3• + H• BDE(CH3-H)
Cl2 → 2Cl• BDE(Cl2)\]
H• + Cl• → HCl -BDE(HCl)
CH3• + Cl• → CH3Cl -BDE(CH3-Cl)
---------------------------------------------------
C H4 + C l2 → C H3 C l + H C l (6.8.6)

ΔH = BDE(R − H ) + BDE(C l2 ) − BDE(H C l) − BDE(C H3 − C l) (6.8.7)

Because reaction enthalpy is a state function, it does not matter what reactions are combined to make up the overall process
using Hess's Law. However, BDEs are convenient to use because they are readily available.

Alternatively, BDEs can be used to assess individual steps of a mechanism. For example, an important step in free radical
chlorination of alkanes is the abstraction of hydrogen from the alkane to form a free radical.
RH + Cl• → R• + HCl
The energy change for this step is equal to the difference in the BDEs in RH and HCl

ΔH = BDE(R − H ) − BDE(H C l) (6.8.8)

This relationship shows that the hydrogen abstraction step is more favorable when BDE(R-H) is smaller. The difference in energies
accounts for the selectivity in the halogenation of hydrocarbons with different types of C-H bonds.
Table 6.8.1: Representative C-H BDEs in Organic Molecules
R-H Do, kJ/mol D298, kJ/mol R-H Do, kJ/mol D298, kJ/mol

CH3-H 432.7±0.1 439.3±0.4 H2C=CH-H 456.7±2.7 463.2±2.9

CH3CH2-H 423.0±1.7 C6H5-H 465.8±1.9 472.4±2.5

(CH3)2CH-H 412.5±1.7 HCCH 551.2±0.1 557.8±0.3

(CH3)3C-H 403.8±1.7

H2C=CHCH2-H 371.5±1.7

HC(O)-H 368.6±0.8 C6H5CH2-H 375.3±2.5

CH3C(O)-H 374.0±1.2

Trends in C-H BDEs

It is important to remember that C-H BDEs refer to the energy it takes to break the bond, and is the difference in energy between
the reactants and the products. Therefore, it is not appropriate to interpret BDEs solely in terms of the "stability of the radical
products" as is often done.
Analysis of the BDEs shown in the table above shows that there are some systematic trends:

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 1. BDEs vary with hybridization: Bonds with sp3 hybridized carbons are weakest and bonds with sp hybridized carbons are
much stronger. The vinyl and phenyl C-H bonds are similar, reflecting their sp2 hybridization. The correlation with
hybridization can be viewed as a reflection of the C-H bond lengths. Longer bonds formed with sp3 orbitals are consequently
weaker. Shorter bonds formed with orbitals that have more s-character are similarly stronger.
2. C-H BDEs vary with substitution: Among sp3 hybridized systems, methane has the strongest C-H bond. C-H bonds on
primary carbons are stronger than those on secondary carbons, which are stronger than those on tertiary carbons.

Interpretation of C-H BDEs for sp3 Hybridized Carbons

The interpretation of the BDEs in saturated molecules has been subject of recent controversy. As indicated above, the variation in
BDEs with substitution has traditionally been interpreted as reflecting the stabilities of the alkyl radicals, with the assessment that
more highly substituted radicals are more stable, as with carbocations. Although this is a popular explanation, it fails to account fo
the fact the bonds to groups other than H do not show the same types of variation.

R BDE(R-CH3) BDE(R-Cl) BDE(R-Br) BDE(R-OH)

CH3- 377.0±0.4 350.2±0.4 301.7±1.3 385.3±0.4

CH3CH2- 372.4±1.7 354.8±2.1 302.9±2.5 393.3±1.7

(CH3)2CH- 370.7±1.7 356.5±2.1 309.2±2.9 399.6±1.7

(CH3)3C- 366.1±1.7 355.2±2.9 303.8±2.5 400.8±1.7

Therefore, although C-CH3 bonds get weaker with more substitution, the effect is not nearly as large as that observed with C-H
bonds. The strengths of C-Cl and C-Br bonds are not affected by substitution, despite the fact that the same radicals are formed as
when breaking C-H bonds, and the C-OH bonds in alcohols actually increase with more substitution.
Gronert has proposed that the variation in BDEs is alternately explained as resulting from destabilization of the reactants due to
steric repulsion of the substituents, which is released in the nearly planar radicals.1 Considering that BDEs reflect the relative
energies of reactants and products, either explanation can account for the trend in BDEs.
Another factor that needs to be considered is the electronegativity. The Pauling definition of electronegativity says that the bond
dissociation energy between unequal partners is going to be dependent on the difference in electrongativities, according to the
expression
Do (A − A) + Do (B − B)
2
Do (A − B) = + (XA − XB ) (6.8.9)
2

where X and X are the electronegativities and the bond energies are in eV. Therefore, the variation in BDEs can be interpreted
A B

as reflecting variation in the electronegativities of the different types of alkyl fragments.

There is likely some merit in all three interpretations. Since Gronert's original publication of his alternate explanation, there have
been many desperate attempts to defend the radical stability explanation.

References
1. Gronert, S. J. Org. Chem. 2006, 13, 1209

Further Reading
MasterOrganicChemistry
Bond Strengths And Radical Stability

Exercises
1. Given that ΔH° for the reaction
CH4 (g) + 4F2 (g) → CF4 (g) + 4HF (g)
is −1936 kJ, use the following data to calculate the average bond energy of the C-F bonds in CF4.

Bond Average Bond Energy

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 C−H 413 kJ · mol−1

F−F 155 kJ · mol−1

H−F 567 kJ · mol−1

2. Calculate ΔH° for the reactions given below.

a. CH3CH2OCH3 + HI -> CH3CH2OH + CH3I
b. CH3Cl + NH3 -> CH3NH2 + HCl

Answers:
1. Bonds broken:
(413 kJ)
4 mol C-H bonds × = 1652 kJ
(1 mol)

(155 kJ)
4 mol F-F bonds × = 620 kJ
(1 mol)

Bonds formed:
(x kJ)
4 mol CF bonds × = 4x kJ
(1 mol)

(where x = the average energy of one mole of C-F bonds in CF4, expressed in kJ)
(567 kJ)
4 mol H-F bonds × = 2268 kJ
(1 mol)

ΔH ° = ΔH °(bonds broken) − ΔH °(bonds formed)

= (1652 kJ + 620 kJ) − (4x + 2268 kJ)

= 1652 kJ + 620 kJ − 4x − 2268 kJ

= −1936 kJ

Thus,
4x = 1936 kJ − 2268 kJ + 620 kJ + 1652 kJ

= 1940 kJ

and
1940 kJ
x =
4 mol
−1
= 385 kJ ⋅ mol

The average energy of a C-F bond in CF4 is 385 kJ · mol-1

2. a. CH3CH2OCH3 + HI → CH3CH2OH + CH3I
Reactant bonds broken D Product bonds formed D

CH CH O−CH 339 kJ/mol CH CH O−H 436 kJ/mol

3 2 3 3 2

H−I 298 kJ/mol CH −I 234 kJ/mol

3
$$ $$
637 kJ/mol 670 kJ/mol

∘
ΔH = Dbonds broken + Dbonds formed

= 637 kJ/mol − 670 kJ/mol

= −33 kJ/mol

b. CH3Cl + NH3 → CH3NH2 + HCl

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 Reactant bonds broken D Product bonds formed D

CH −Cl 351 kJ/mol CH −NH 335 kJ/mol

3 3 2

NH −H 449 kJ/mol H−Cl 432 kJ/mol

2
$$ $$
800 kJ/mol 767 kJ/mol

∘
ΔH = Dbonds broken + Dbonds formed

= 800 kJ/mol − 767 kJ/mol

= +33 kJ/mol

Contributors and Attributions

Prof. Paul G. Wenthold (Purdue University)

6.8: Describing a Reaction - Bond Dissociation Energies is shared under a CC BY-SA 4.0 license and was authored, remixed, and/or curated by
Steven Farmer & Dietmar Kennepohl.

6.8.5 https://chem.libretexts.org/@go/page/31443
6.9: Describing a Reaction - Energy Diagrams and Transition States
 Objectives

After completing this section, you should be able to

1. sketch the reaction energy diagram for a single-step reaction, given some indication of whether the reaction is fast or slow,
exothermic or endothermic.
2. interpret the reaction energy diagram for a single-step process (e.g., use the diagram to decide whether the reaction is
exothermic or endothermic).
3. suggest possible transition-state structures for simple one-step processes.
4. assess the likelihood of a reaction occurring at room temperature, given the value of the activation energy ΔG‡.

 Key Terms
Make certain that you can define, and use in context, the key terms below.
activation energy, ΔG‡
reaction energy diagram
transition state

 Study Notes

You may have been taught to use the term “activated complex” rather than “transition state,” as the two are often used
interchangeably. Similarly, the activation energy of a reaction is often represented by the symbol Eact or Ea.

You may recall from general chemistry that it is often convenient to describe chemical reactions with energy diagrams. In an energy
diagram, the vertical axis represents the overall energy of the reactants, while the horizontal axis is the ‘reaction coordinate’,
tracing from left to right the progress of the reaction from starting compounds to final products. The energy diagram for a typical
one-step reaction might look like this:

Despite its apparent simplicity, this energy diagram conveys some very important ideas about the thermodynamics and kinetics of
the reaction. Recall that when we talk about the thermodynamics of a reaction, we are concerned with the difference in energy
between reactants and products, and whether a reaction is ‘downhill’ (exergonic, energy releasing) or ‘uphill (endergonic, energy
absorbing). When we talk about kinetics, on the other hand, we are concerned with the rate of the reaction, regardless of whether it
is uphill or downhill thermodynamically.
First, let’s review what this energy diagram tells us about the thermodynamics of the reaction illustrated by the energy diagram
above. The energy level of the products is lower than that of the reactants. This tells us that the change in standard Gibbs Free
Energy for the reaction (ΔG˚rnx) is negative. In other words, the reaction is exergonic, or ‘downhill’. Recall that the ΔG˚rnx term
encapsulates both ΔH˚rnx, the change in enthalpy (heat) and ΔS˚rnx , the change in entropy (disorder):

ΔG˚ = ΔH ˚ − T ΔS˚ (6.9.1)

where T is the absolute temperature in Kelvin. For chemical processes where the entropy change is small (~0), the enthalpy change
is essentially the same as the change in Gibbs Free Energy. Energy diagrams for these processes will often plot the enthalpy (H)

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instead of Free Energy for simplicity.
The standard Gibbs Free Energy change for a reaction can be related to the reaction's equilibrium constant (\(K_{eq}\_) by a
simple equation:

ΔG˚ = −RT ln Keq (6.9.2)

where:
Keq = [product] / [reactant] at equilibrium
R = 8.314 J×K-1×mol-1 or 1.987 cal× K-1×mol-1
T = temperature in Kelvin (K)
If you do the math, you see that a negative value for ΔG˚rnx (an exergonic reaction) corresponds - as it should by intuition - to Keq
being greater than 1, an equilibrium constant which favors product formation.
In a hypothetical endergonic (energy-absorbing) reaction the products would have a higher energy than reactants and thus ΔG˚rnx
would be positive and Keq would be less than 1, favoring reactants.

Now, let's move to kinetics. Look again at the energy diagram for exergonic reaction: although it is ‘downhill’ overall, it isn’t a
straight downhill run.

First, an ‘energy barrier’ must be overcome to get to the product side. The height of this energy barrier, you may recall, is called the
‘activation energy’ (ΔG ‡ ). The activation energy is what determines the kinetics of a reaction: the higher the energy hill, the
slower the reaction. At the very top of the energy barrier, the reaction is at its transition state (TS), which is the point at which the
bonds are in the process of breaking and forming. The transition state is an ‘activated complex’: a transient and dynamic state that,
unlike more stable species, does not have any definable lifetime. It may help to imagine a transition state as being analogous to the
exact moment that a baseball is struck by a bat. Transition states are drawn with dotted lines representing bonds that are in the
process of breaking or forming, and the drawing is often enclosed by brackets. Here is a picture of a likely transition state for a
substitution reaction between hydroxide and chloromethane:
− −
C H3 C l + H O → C H3 OH + C l (6.9.3)

‡
H
𝛅− 𝛅−
H O C Cl
H H

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This reaction involves a collision between two molecules: for this reason, we say that it has second order kinetics. The rate
expression for this type of reaction is:
rate = k[reactant 1][reactant 2]
. . . which tells us that the rate of the reaction depends on the rate constant k as well as on the concentration of both reactants. The
rate constant can be determined experimentally by measuring the rate of the reaction with different starting reactant concentrations.
The rate constant depends on the activation energy, of course, but also on temperature: a higher temperature means a higher k and a
faster reaction, all else being equal. This should make intuitive sense: when there is more heat energy in the system, more of the
reactant molecules are able to get over the energy barrier.
Here is one more interesting and useful expression. Consider a simple reaction where the reactants are A and B, and the product is
AB (this is referred to as a condensation reaction, because two molecules are coming together, or condensing). If we know the
rate constant k for the forward reaction and the rate constant kreverse for the reverse reaction (where AB splits apart into A and B),
we can simply take the quotient to find our equilibrium constant K : eq

This too should make some intuitive sense; if the forward rate constant is higher than the reverse rate constant, equilibrium should
lie towards products.

Exercises
Questions
Q6.9.1
Which reaction is faster, ΔG‡ = + 55 kJ/mol or ΔG‡ = + 75 kJ/mol?
Solutions
S6.9.1
The + 55 kJ/mol reaction is the faster reaction.
6.9: Describing a Reaction - Energy Diagrams and Transition States is shared under a CC BY-SA 4.0 license and was authored, remixed, and/or
curated by Steven Farmer, Dietmar Kennepohl, Krista Cunningham, Tim Soderberg, & Tim Soderberg.

6.9.3 https://chem.libretexts.org/@go/page/31444
6.10: Describing a Reaction- Intermediates
 Objectives

After completing this section, you should be able to

1. explain the difference between a transition state and an intermediate.
2. draw a reaction energy diagram for a given multistep process.
3. interpret the reaction energy diagram of a multistep process (e.g., determine which of the steps is rate-determining).

 Key Terms
Make certain that you can define, and use in context, the key term below.
reaction intermediate

 Study Notes

Each step in a multistep reaction has its own activation energy. The overall activation energy is the difference in energy
between the reactants and the transition state of the slowest (rate-determining) step. The rate-determining step, that is, the one
that controls the overall rate of reaction, is the step with the highest activation energy.

A second model for a nucleophilic substitution reaction is called the 'dissociative', or 'SN1' mechanism: in this picture, the C-X
bond breaks first, before the nucleophile approaches:
R R

R1 C C
R2 X
R1 R 2

This results in the formation of a carbocation: because the central carbon has only three bonds, it bears a formal charge of +1.
Recall that a carbocation should be pictured as sp2 hybridized, with trigonal planar geometry. Perpendicular to the plane formed by
the three sp2 hybrid orbitals is an empty, unhybridized p orbital.
empty p orbital
R
C
R1 R2

In the second step of this two-step reaction, the nucleophile attacks the empty, 'electron hungry' p orbital of the carbocation to form
a new bond and return the carbon to tetrahedral geometry.
R Nu R R
C C + X C R inversion
R1 X
R2 Nu R2
1
R1 R2

OR

R Nu R
C + X R1 C retention
R2 Nu
R1 R2

We saw that SN2 reactions result specifically in inversion of stereochemistry at the electrophilic carbon center. What about the
stereochemical outcome of SN1 reactions? In the model SN1 reaction shown above, the leaving group dissociates completely from
the vicinity of the reaction before the nucleophile begins its attack. Because the leaving group is no longer in the picture, the
nucleophile is free to attack from either side of the planar, sp2-hybridized carbocation electrophile. This means that about half the
time the product has the same stereochemical configuration as the starting material (retention of configuration), and about half the
time the stereochemistry has been inverted. In other words, racemization has occurred at the carbon center. As an example, the
tertiary alkyl bromide below would be expected to form a racemic mix of R and S alcohols after an SN1 reaction with water as the
incoming nucleophile.
H3 C Br O H3 C OH HO CH3
H H
+ + H Br

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  Exercise 6.10.1

Draw the structure of the intermediate in the two-step nucleophilic substitution reaction above.

Answer

The SN1 reaction we see an example of a reaction intermediate, a very important concept in the study of organic reaction
mechanisms that was introduced earlier in the module on organic reactivity Recall that many important organic reactions do not
occur in a single step; rather, they are the sum of two or more discreet bond-forming / bond-breaking steps, and involve transient
intermediate species that go on to react very quickly. In the SN1 reaction, the carbocation species is a reaction intermediate. A
potential energy diagram for an SN1 reaction shows that the carbocation intermediate can be visualized as a kind of valley in the
path of the reaction, higher in energy than both the reactant and product but lower in energy than the two transition states.

R Nu R R
C C + X C R
R1 X Nu 1
R2 R1 R2 R2

R I P

 Exercise 6.10.2

Draw structures representing TS1 and TS2 in the reaction above. Use the solid/dash wedge convention to show three
dimensions.

Answer

Recall that the first step of the reaction above, in which two charged species are formed from a neutral molecule, is much the
slower of the two steps, and is therefore rate-determining. This is illustrated by the energy diagram, where the activation energy for

6.10.2 https://chem.libretexts.org/@go/page/31445
the first step is higher than that for the second step. Also recall that an SN1 reaction has first order kinetics, because the rate
determining step involves one molecule splitting apart, not two molecules colliding
We come now to the subject of catalysis. Our hypothetical bowl of sugar (from section 6.2) is still stubbornly refusing to turn into
carbon dioxide and water, even though by doing so it would reach a much more stable energy state. There are, in fact, two ways
that we could speed up the process so as to avoid waiting several millennia for the reaction to reach completion. We could supply
enough energy, in the form of heat from a flame, to push some of the sugar molecules over the high energy hill. Heat would be
released from the resulting exothermic reaction, and this energy would push more molecules over their energy hills, and so on - the
sugar would literally burn up.
A second way to make the reaction go faster is to employ a catalyst. You probably already know that a catalyst is an agent that
causes a chemical reaction to go faster by lowering its activation energy.

How might you catalyze the conversion of sugar to carbon dioxide and water? It’s not too hard – just eat the sugar, and let your
digestive enzymes go to work catalyzing the many biochemical reactions involved in breaking it down. Enzymes are proteins, and
are very effective catalysts. ‘Very effective’ in this context means very specific, and very fast. Most enzymes are very selective
with respect to reactant molecules: they have evolved over millions of years to catalyze their specific reactions. An enzyme that
attaches a phosphate group to glucose, for example, will not do anything at all to fructose (the details of these reactions are
discussed in section 10.2B).
OH OH
O OH O OH
glucose kinase

HO OH HO OH
OH OH

glucose glucose 6-phosphate

HO
HO
O glucose kinase
OH no reaction

HO OH

fructose

Glucose kinase is able to find and recognize glucose out of all of the other molecules floating around in the 'chemical soup' of a
cell. A different enzyme, fructokinase, specifically catalyzes the phosphorylation of fructose.
We have already learned (section 3.9) that enzymes are very specific in terms of the stereochemistry of the reactions that they
catalyze . Enzymes are also highly regiospecific, acting at only one specific part of a molecule. Notice that in the glucose kinase
reaction above only one of the alcohol groups is phosphorylated.
Finally, enzymes are capable of truly amazing rate acceleration. Typical enzymes will speed up a reaction by anywhere from a
million to a billion times, and the most efficient enzyme currently known to scientists is believed to accelerate its reaction by a
factor of about 1017 (see Chemical and Engineering News, March 13, 2000, p. 42 for an interesting discussion about this enzyme,
orotidine monophosphate decarboxylase).
We will now begin an exploration of some of the basic ideas about how enzymes accomplish these amazing feats of catalysis, and
these ideas will be revisited often throughout the rest of the text as we consider various examples of enzyme-catalyzed organic

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reactions. But in order to begin to understand how enzymes work, we will first need to learn (or review, as the case may be) a little
bit about protein structure.

Exercises
Questions
Q6.10.1
Draw an energy diagram with a exergonic first step and an endergonic second step. Label the diagram.
Solutions
S6.10.1

6.10: Describing a Reaction- Intermediates is shared under a CC BY-SA 4.0 license and was authored, remixed, and/or curated by Steven Farmer,
Dietmar Kennepohl, Krista Cunningham, Tim Soderberg, & Tim Soderberg.

6.10.4 https://chem.libretexts.org/@go/page/31445
6.11: A Comparison between Biological Reactions and Laboratory Reactions
 Objectives
No objectives have been identified for this section

 Key Terms
Make certain that you can define, and use in context, the key term below.
enzyme

 Study Notes

This section is a brief (but perhaps interesting) overview of some of the key differences between reactions performed in the lab
and those in living systems. At this point, do not concern yourself with memorizing large biological molecules and reactions.

The active site

A critical element in the three-dimensional structure of any enzyme is the presence of an ‘active site’, which is a pocket, usually
located in the interior of the protein, that serves as a docking point for the enzyme’s substrate(s) (‘substrate’ is the term that
biochemists use for a reactant molecule in an enzyme-catalyzed reaction). It is inside the active site pocket that enzymatic catalysis
occurs. Shown below is an image of the glycolytic enzyme fructose-1,6-bisphosphate aldolase, with its substrate bound inside the
active site pocket.

When the substrate binds to the active site, a large number of noncovalent interactions form with the amino acid residues that line
the active site. The shape of the active site, and the enzyme-substrate interactions that form as a result of substrate binding, are
specific to the substrate-enzyme pair: the active site has evolved to 'fit' one particular substrate and to catalyze one particular
reaction. Other molecules do not fit in this active site nearly so well as fructose 1,6-bisphosphate.
Here are two close-up views of the same active site pocket, showing some of the specific hydrogen-bonding interactions between
the substrate and active site amino acids. The first image below is a three-dimensional rendering directly from the crystal structure
data. The substrate is shown in 'space-filling' style, while the active site amino acids are shown in the 'ball and stick' style.
Hydrogens are not shown. The color scheme is grey for carbon, red for oxygen, blue for nitrogen, and orange for phosphorus.

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Below is a two-dimensional picture of the substrate (colored blue) surrounded by hydrogen-bonding active site amino acids. Notice
that both main chain and side chain groups contribute to hydrogen bonding: in this figure, main chain H-bonding groups are
colored purple, and side chain H-bonding groups are colored green.

Arg Arg
O Lys Ser
N
N H 2N Lys
H H 2N NH2 O
O H
H H NH2
H O O O H
O
N H O P O Ser
O O P O
H O
Ser O O O H N O
O H H H H
N O NH2 O
Ser Arg
O Glu Lys

Looking at the last three images should give you some appreciation for the specific manner in which a substrate fits inside its active
site.

Transition state stabilization

One of the most important ways that an enzyme catalyzes any given reaction is through entropy reduction: by bringing order to a
disordered situation (remember that entropy is a component of Gibbs Free Energy, and thus a component of the activation energy).
Let’s turn again to our previous example (from section 6.1C) of a biochemical nucleophilic substitution reaction, the methylation of
adenosine in DNA. The reaction is shown below with non-reactive sections of the molecules depicted by variously shaped 'bubbles'
for the sake of simplicity.

H
H H
N + S H C H +
N
H S
C
H H
H
adenosine (DNA) SAM

In order for this reaction to occur, the two substrates (reactants) must come into contact in precisely the right way. If they are both
floating around free in solution, the likelihood of this occurring is very small – the entropy of the system is simply too high. In
other words, this reaction takes place very slowly without the help of a catalyst.
Here’s where the enzyme’s active site pocket comes into play. It is lined with various functional groups from the amino acid main
and side chains, and has a very specific three-dimensional architecture that has evolved to bind to both of the substrates. If the
SAM molecule, for example, diffuses into the active site, it can replace its (favorable) interactions with the surrounding water
molecules with (even more favorable) new interactions with the functional groups lining the active site.

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 H
H C S
H

Depiction of SAM bound in active site of enzyme

In a sense, SAM is moving from one solvent (water) to another 'solvent' (the active site), where many new energetically favorable
interactions are possible. Remember: these new contacts between SAM and the active site groups are highly specific to SAM and
SAM alone – no other molecule can ‘fit’ so well in this precise active site environment, and thus no other molecule will be likely to
give up its contacts to water and bind to the active site.
The second substrate also has a specific spot reserved in the active site. (Because in this case the second substrate is a small
segment of a long DNA molecule, the DNA-binding region of the active site is more of a 'groove' than a 'pocket').

H
H
H C S
N
H
H

So now we have both substrates bound in the active site. But they are not just bound in any random orientation – they are
specifically positioned relative to one another so that the nucleophilic nitrogen is held very close to the electrophilic carbon, with a
free path of attack. What used to be a very disordered situation – two reactants diffusing freely in solution – is now a very highly
ordered situation, with everything set up for the reaction to proceed. This is what is meant by entropy reduction: the entropic
component of the energy barrier has been lowered.
Looking a bit deeper, though, it is not really the noncovalent interaction between enzyme and substrate that are responsible for
catalysis. Remember: all catalysts, enzymes included, accelerate reactions by lowering the energy of the transition state. With this
in mind, it should make sense that the primary job of an enzyme is to maximize favorable interactions with the transition state, not
with the starting substrates. This does not imply that enzyme-substrate interactions are not strong, rather that enzyme-TS
interactions are far stronger, often by several orders of magnitude. Think about it this way: if an enzyme were to bind to (and
stabilize) its substrate(s) more tightly than it bound to (and stabilized) the transition state, it would actually slow down the reaction,
because it would be increasing the energy difference between starting state and transition state. The enzyme has evolved to
maximize favorable noncovalent interactions to the transition state: in our example, this is the state in which the nucleophilic
nitrogen is already beginning to attack the electrophilic carbon, and the carbon-sulfur bond has already begun to break.
‡

HH
H S
C
N
H H

enzyme binds best to

the transition state

In many enzymatic reactions, certain active site amino acid residues contribute to catalysis by increasing the reactivity of the
substrates. Often, the catalytic role is that of acid and/or base. In our DNA methylation example, the nucleophilic nitrogen is
deprotonated by a nearby aspartate side chain as it begins its nucleophilic attack on the methyl group of SAM. We will study
nucleophilicity in greater detail in chapter 8, but it should make intuitive sense that deprotonating the amine increases the electron
density of the nitrogen, making it more nucleophilic. Notice also in the figure below that the main chain carbonyl of an active site
proline forms a hydrogen bond with the amine, which also has the effect of increasing the nitrogen's electron density and thus its
nucleophilicity (Nucleic Acids Res. 2000, 28, 3950).

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 N
enz enz
N
enz enz
O
H O S
H
H C S
N
H H
H
N
HO O
CH3
O O

enz
enz

How does our picture of enzyme catalysis apply to multi-step reaction mechanisms? Although the two-step nucleophilic
substitution reaction between 2-chloro-2-methylpropane and the cyanide anion is not a biologically relevant process, let’s pretend
just for the sake of illustration that there is a hypothetical enzyme that catalyzes this reaction.

CN
H 3C CH3 H 3C CH3 H 3C CH3
C C + Cl
H 3C Cl (slow) (fast) H 3C CN
CH3

The same basic principles apply here: the enzyme binds best to the transition state. But therein lies the problem: there are two
transition states! To which TS does the enzyme maximize its contacts?
Recall that the first step – the loss of the chloride leaving group to form the carbocation intermediate – is the slower, rate-limiting
step. It is this step that our hypothetical enzyme needs to accelerate if it wants to accelerate the overall reaction, and it is thus the
energy of TS1 that needs to be lowered.
‡
H3C CH3
C Cl
𝛅+ 𝛅−
H 3C

By Hammond’s postulate, we also know that the intermediate I is a close approximation of TS1. So the enzyme, by stabilizing the
intermediate, will also stabilize TS1 (as well as TS2) and thereby accelerate the reaction.

If you read scientific papers about enzyme mechanisms, you will often see researchers discussing how an enzyme stabilizes a
reaction intermediate. By virtue of Hammond's postulate, they are, at the same time, talking about how the enzyme lowers the
energy of the transition state.
An additional note: although we have in this section been referring to SAM as a 'substrate' of the DNA methylation reaction, it is
also often referred to as a coenzyme, or cofactor. These terms are used to describe small (relative to protein and DNA) biological
organic molecules that bind specifically in the active site of an enzyme and help the enzyme to do its job. In the case of SAM, the
job is methyl group donation. In addition to SAM, we will see many other examples of coenzymes in the coming chapters, a
number of which - like ATP (adenosine triphosphate), coenzyme A, thiamine, and flavin - you have probably heard of before. The
full structures of some common coenzymes are shown in table 6 in the tables section.

6.11: A Comparison between Biological Reactions and Laboratory Reactions is shared under a CC BY-SA 4.0 license and was authored, remixed,
and/or curated by Steven Farmer, Dietmar Kennepohl, Krista Cunningham, Tim Soderberg, & Tim Soderberg.

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6.S: An Overview of Organic Reactions (Summary)
Concepts & Vocabulary
6.1: Kinds of Organic Reactions
Addition reactions increase the number of sigma bonds in a molecule.
Elimination reactions reduce the number of sigma bonds in a molecule.
Substitution reactions incorporate replacement of an atom or group with another.
Rearrangement reactions cause a molecule to be converted to a constitutional isomer without gaining or losing any atoms.
6.2: How Organic Reactions Occur: Mechanisms
A reaction mechanism describes movement of electrons by using curved arrows to show bonds that are breaking and forming.
Homolysis occurs when a bond breaks with each atom keeping one electron.
Heterolysis occurs when a bond breaks and both electrons remain with one of the atoms.
Some reactions occur in more than one step with a reactive intermediate formed briefly on the way to the new product.
Reactive intermediates can be charged species such as carbocations and carbanions or uncharged species such as radicals.
In organic chemistry Lewis acids are more often referred to as electrophiles, having an affinity for an electron pair.
In organic chemistry Lewis bases are more often referred to as nucleophiles, having an electron pair that is available to bond to
an electrophile.
Ionic reactions involve charged species.
Polar reactions involve bonds with unequally shared electrons.
6.3: Radical Reactions
Radical chain reactions have three distinct phases: initiation, propagation and termination.
Initiation causes radicals to be created from non-radical species.
During the Propagation phase, radicals react with stable molecules to form new radicals.
Termination occurs when two radicals react together to form a stable molecule.
6.4: Polar Reactions
Carbon when bonded to a halogen, oxygen, nitrogen, sulfur, or metal has a partial positive charge. This allows these carbons to
react with many nucleophiles.
For carbonyl groups bond polarity is reinforced by resonance making the carbon even more positive than in other molecules.
This makes carbonyl groups prone to addition and substitution reactions with nucleophiles.
Nucleophiles have electron rich atoms that are able to donate a pair of electrons.
In nucleophilic substitution reactions, the electrophile is typically carbon bonded to a more electronegative atom.
6.5: An Example of a Polar Reaction: Addition of HBr to Ethylene
Alkene addition reaction with HBr occurs through the pi bond reacting as a nucleophile and abstracting a proton from the acid.
This creates a carbocation intermediate which reacts with the bromide ion to form the final product.
Reaction rates for this alkene addition reaction increase with larger halogens and more substituted alkenes.
Markovnikov's Rule states that addition reactions of unsymmetrical alkenes yield the more substituted product.
6.6: Using Curved Arrows in Polar Reaction Mechanisms
Curved arrows in mechanism drawings always represent electrons moving, starting at either a bond or lone pair of electrons.
Electrons flow from electron rich to electron poor.
6.7: Describing a Reaction: Equilibria, Rates, and Energy Changes
Exergonic reactions have a negative free energy meaning they are thermodynamically favorable and give off energy.
Endergonic reactions have a positive free energy and require energy from the surroundings to occur.
6.8: Describing a Reaction: Bond Dissociation Energies
Bond dissociation energy for a molecule is the difference in enthalpy of formation (homolytic) for the products and reactants.
Bond dissociation energies are independent of path of reaction, so they do not give direct information on mechanisms.
However, they can be used to evaluate the results of individual steps of a mechanism.

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 Bond dissociation energies show that sigma bonds formed with sp hybridized carbon are stronger than sp2 which are stronger
than bonds formed with sp3 carbons.
Bond dissociation energies show that carbon-hydrogen bonds on primary carbons are stronger than secondary, which are
stronger than tertiary.
6.9: Describing a Reaction: Energy Diagrams and Transition States
Reaction coordinate diagrams are a special type of energy diagram that has the reaction coordinate (or reaction progress) on
the x-axis.
Thermodynamics of a reaction is conveyed on a reaction coordinate diagram by the difference in energy between the reactants
and products.
Activation energy is the energy barrier to a reaction occurring.
A transition state is the highest energy point during the process of bonds forming and breaking in a reaction step.
Kinetics of a reaction is conveyed on a reaction coordinate diagram by the difference in energy between the reactants and
transition state.
A rate expression relates rate to the rate constant and concentration of reactants.
6.10: Describing a Reaction: Intermediates
A reaction intermediate is a short-lived species that goes on to react in a subsequent reaction step.
Reaction intermediates appear as a local minimum (or valley) on a reaction coordinate diagram.
Catalysts cause reaction rates to increase by lowing activation energy.
6.11: A Comparison between Biological Reactions and Laboratory Reactions
An enzyme active site is the location where the enzyme interacts with its substrate and where catalysis occurs.
Substrates are reactant molecules in enzymatic reactions.

Skills to Master

Skill 6.1 Identify organic reactions by type (addition, elimination, substitution, rearrangement).
SKil 6.2 Draw homolytic and heterolytic bond breaking as part of reaction mechanisms.
Skill 6.3 Identify radical and ionic reactions.
Skill 6.4 Identify and write out steps in a typical radical substitution reaction (initiation, propagation, termination).
Skill 6.5 Identify polarity of bonds in organic molecules.
Skill 6.6 Use curved arrows to indicate movement of electrons in resonance and reaction mechanisms.
Skill 6.7 Predict whether a chemical species will act as an electrophile or nucleophile.
Skill 6.8 Write an equilibrium expression for a reaction.
Skill 6.9 Determine the direction of a reaction based on the equilibrium constant.
Skill 6.10 Explain how rate and equilibrium are related to ΔG° and Keq.
Skill 6.11 Calculate bond dissociation energy given enthalpies of formation for reactants and products.
Skill 6.12 Describe order of bond strength based on bond dissociation energy.
Skill 6.13 Explain activation energy, kinetics, thermodynamics and transition states based on energy diagrams (reaction
coordinate diagrams).
Skill 6.14 Predict possible transition state structures for single reaction steps.
Skill 6.15 Differentiate between transition states and intermediates.
Skill 6.16 Draw a reaction coordinate diagram for a given multi-step process.
Skill 6.17 Interpret a reaction coordinate diagram for a multi-step process.
Skill 6.18 Briefly explain how enzymes catalyze reactions.

Memorization Tasks
MT 6.1 Memorize that arrows in reaction mechanisms always define movement of electrons.
MT 6.2 Memorize the relative electronegativities of common atoms (necessary for determining polarity of bonds).
MT 6.3 Memorize the equations that relate equilibrium, free energy, enthalpy and entropy.
ΔGº=–RTlnK

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