CHEM 26505:

ORGANIC CHEMISTRY I

Mark Lipton
Purdue University
 Purdue University
Chem 26505: Organic Chemistry I

Mark Lipton
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TABLE OF CONTENTS
Licensing

Chapter 1. Electronic Structure and Chemical Bonding

1.1: Electronic Configuration of Atoms
1.2: The Octet Rule and Covalent Bonding
1.3: Valence electrons and open valences
1.4: Formal Charge
1.5: Resonance
1.6: Electronegativity and Bond Polarization
1.7: Atomic Orbitals and Covalent Bonding
1.8: Hybridization
1.9: Representation of Molecular Structure
1.10: Pi Conjugation
1.11: Aromaticity

Chapter 2. Functional Groups and Nomenclature

2.1: Alkanes
2.1B: Cycloalkanes
2.2: Alkenes
2.3: Alkynes
2.4: Arenes
2.5: Functional Groups
2.5: Alcohols
2.6: Ethers, Epoxides and Sulfides
2.7: Amines
2.8: Aldehydes and Ketones
2.9: Carboxylic Acids
2.10: Esters, Amides, Acid Halides, Anhydrides and Nitriles
Appendix - IUPAC Nomenclature Rules

Chapter 3. Stereochemistry
3.1 Stereoisomerism
3.2 Conformations of Alkanes
3.3 Conformation of Cyclohexane
3.4 Chirality
3.5 Enantiomers
3.6 Cahn-Ingold Prelog Rules
3.7 Diastereomers
3.8 Meso Isomers
3.9 Cis/Trans Isomerism

Chapter 4. Intermolecular Forces and Physical Properties

4.1 Bond Polarity and Molecular Dipoles
4.2 Intermolecular Forces
4.3 Boiling Points
4.4 Solubility

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 4.5 Chromatography

Chapter 5. Spectroscopy
5.1 Infrared Spectroscopy
5.2 Mass Spectrometry
5.3 Nuclear Magnetic Resonance (NMR) Spectroscopy
5.4 Ultraviolet (UV) Spectroscopy
5.5 Polarimetry

Chapter 6. Reactive Intermediates

6.1 Carbocations
6.2: Carbanions
6.3 Free Radicals

Chapter 7. Reactivity and Electron Movement

7.1 Nucleophiles and Electrophiles
7.2 How Electrons Move
7.3 Basics of Thermodynamics and Kinetics
7.4 Kinetics
7.5 Product Distributions
7.6 Hammond's Postulate

Chapter 8. Acid-Base Reactions

8.1 Brønsted Acidity and Basicity
8.2 Factors Affecting Brønsted Acidity
8.3: pKa Values
8.4 Solvent Effects

Chapter 9. Isomerization Reactions

9.1: Keto-Enol Tautomerization
9.2: 1,2-Shifts in Carbocations

Course Content
I. Chemical Bonding and Electronic Structure
II. Functional groups and Nomenclature
III. Stereochemistry
IV. Intermolecular interactions and physical properties
V. Reactive intermediates: carbocations, carbanions, free radicals
VI. Spectroscopy
VII. Reactivity and the movement of electrons
VIII. Acid-Base Reactivity

Index

Glossary

Detailed Licensing

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Licensing
A detailed breakdown of this resource's licensing can be found in Back Matter/Detailed Licensing.

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 CHAPTER OVERVIEW

Chapter 1. Electronic Structure and Chemical Bonding

Purdue CHM 26505: Organic

Chemistry for Chemistry Majors (1st
Semester)
Fall 2014: Prof. Mark Lipton

Template:HideTOC

Topic hierarchy
1.1: Electronic Configuration of Atoms
1.2: The Octet Rule and Covalent Bonding
1.3: Valence electrons and open valences
1.4: Formal Charge
1.5: Resonance
1.6: Electronegativity and Bond Polarization
1.7: Atomic Orbitals and Covalent Bonding
1.8: Hybridization
1.9: Representation of Molecular Structure
1.10: Pi Conjugation
1.11: Aromaticity

Chapter 1. Electronic Structure and Chemical Bonding is shared under a CC BY-NC-SA 4.0 license and was authored, remixed, and/or curated by
LibreTexts.

1
1.1: Electronic Configuration of Atoms
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.

Contributors and Attributions

Sarah Faizi (University of California Davis)

Further Reading

MasterOrganicChemistry
From General Chemistry to Organic
Electrons and Orbitals
Effective Nuclear Charge

Carey 4th Edition On-Line Activity

Atoms, Electrons and Orbitals
Khan Academy
Elements and Atoms
Introduction to the Atom
Atomic Orbitals
Orbitals and Electron Configurations
Electron Configurations
Electron Configurations Part 2
Valence Electrons

Leah4Sci
Electron Configuration Part 1
Electron Configuration Part 2
Intro to Organic Chemistry 1
Intro to Organic Chemistry 2

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Cliffs Notes
Principles of Atomic Structure

Web Pages
Electron Configurations
Electron Configurations and Orbital Diagrams
Visualizing Atomic Orbitals
Videos
Electron Configurations and Orbital Diagrams
Atomic Orbital Video

Tutorial
Chemistry is Easy! Electron Configurations
1.1: Electronic Configuration of Atoms is shared under a CC BY-NC-SA 4.0 license and was authored, remixed, and/or curated by LibreTexts.
Electronic Configurations Intro is licensed CC BY-NC-SA 4.0.

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1.2: The Octet Rule and Covalent Bonding
There are many types of chemical bonds and forces that bind molecules together. The two most basic types of bonds are
characterized as either ionic or covalent. In ionic bonding, atoms transfer electrons to each other. Ionic bonds require at least one
electron donor and one electron acceptor. In contrast, atoms with the same electronegativity share electrons in covalent bonds,
because neither atom preferentially attracts or repels the shared electrons.

Introduction
Ionic bonding is the complete transfer of valence electron(s) between atoms. It is a type of chemical bond that generates two
oppositely charged ions. In ionic bonds, the metal loses electrons to become a positively charged cation, whereas the nonmetal
accepts those electrons to become a negatively charged anion. Ionic bonds require an electron donor, often a metal, and an electron
acceptor, a nonmetal.
Ionic bonding is observed because metals have few electrons in their outer-most orbitals. By losing those electrons, these metals
can achieve noble gas configuration and satisfy the octet rule. Similarly, nonmetals that have close to 8 electrons in their valence
shells tend to readily accept electrons to achieve noble gas configuration. In ionic bonding, more than 1 electron can be donated or
received to satisfy the octet rule. The charges on the anion and cation correspond to the number of electrons donated or received. In
ionic bonds, the net charge of the compound must be zero.

This sodium molecule donates the lone electron in its valence orbital in order to achieve octet configuration. This creates a
positively charged cation due to the loss of electron.

This chlorine atom receives one electron to achieve its octet configuration, which creates a negatively charged anion.
The predicted overall energy of the ionic bonding process, which includes the ionization energy of the metal and electron affinity of
the nonmetal, is usually positive, indicating that the reaction is endothermic and unfavorable. However, this reaction is highly
favorable because of the electrostatic attraction between the particles. At the ideal interatomic distance, attraction between these
particles releases enough energy to facilitate the reaction. Most ionic compounds tend to dissociate in polar solvents because they
are often polar. This phenomenon is due to the opposite charges on each ion.

 Example 1.2.1: Chloride Salts

In this example, the sodium atom is donating its 1 valence electron to the chlorine atom. This creates a sodium cation and a
chlorine anion. Notice that the net charge of the resulting compound is 0.

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 In this example, the magnesium atom is donating both of its valence electrons to chlorine atoms. Each chlorine atom can only
accept 1 electron before it can achieve its noble gas configuration; therefore, 2 atoms of chlorine are required to accept the 2
electrons donated by the magnesium. Notice that the net charge of the compound is 0.

Covalent Bonding
Covalent bonding is the sharing of electrons between atoms. This type of bonding occurs between two atoms of the same element
or of elements close to each other in the periodic table. This bonding occurs primarily between nonmetals; however, it can also be
observed between nonmetals and metals.
If atoms have similar electronegativities (the same affinity for electrons), covalent bonds are most likely to occur. Because both
atoms have the same affinity for electrons and neither has a tendency to donate them, they share electrons in order to achieve octet
configuration and become more stable. In addition, the ionization energy of the atom is too large and the electron affinity of the
atom is too small for ionic bonding to occur. For example: carbon does not form ionic bonds because it has 4 valence electrons, half
of an octet. To form ionic bonds, Carbon molecules must either gain or lose 4 electrons. This is highly unfavorable; therefore,
carbon molecules share their 4 valence electrons through single, double, and triple bonds so that each atom can achieve noble gas
configurations. Covalent bonds include interactions of the sigma and pi orbitals; therefore, covalent bonds lead to formation of
single, double, triple, and quadruple bonds.

 Example 1.2.2: P C l 3

In this example, a phosphorous atom is sharing its three unpaired electrons with three chlorine atoms. In the end product, all four of
these molecules have 8 valence electrons and satisfy the octet rule.

Bonding in Organic Chemistry

Ionic and covalent bonds are the two extremes of bonding. Polar covalent is the intermediate type of bonding between the two
extremes. Some ionic bonds contain covalent characteristics and some covalent bonds are partially ionic. For example, most
carbon-based compounds are covalently bonded but can also be partially ionic. Polarity is a measure of the separation of charge in
a compound. A compound's polarity is dependent on the symmetry of the compound and on differences in electronegativity
between atoms. Polarity occurs when the electron pushing elements, found on the left side of the periodic table, exchanges
electrons with the electron pulling elements, on the right side of the table. This creates a spectrum of polarity, with ionic (polar) at
one extreme, covalent (nonpolar) at another, and polar covalent in the middle.
Both of these bonds are important in organic chemistry. Ionic bonds are important because they allow the synthesis of specific
organic compounds. Scientists can manipulate ionic properties and these interactions in order to form desired products. Covalent
bonds are especially important since most carbon molecules interact primarily through covalent bonding. Covalent bonding allows
molecules to share electrons with other molecules, creating long chains of compounds and allowing more complexity in life.

References
1. Vollhardt, K. Peter C., and Neil E. Schore. Organic Chemistry Structure and Function. New York: W. H. Freeman, 2007.
2. Petrucci, Ralph H. General Chemistry: Principles and Modern Applications. Upper Saddle River, NJ: Pearson Education, 2007.
3. Brown, Theodore L., Eugene H. Lemay, and Bruce E. Bursten. Chemistry: The Central Science. 6th ed. Englewood Cliffs, NJ:
Prentice Hall, 1994.

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Problems
1. Are these compounds ionic or covalent?

2. In the following reactions, indicate whether the reactants and products are ionic or covalently bonded.
a)

b) Clarification: What is the nature of the bond between sodium and amide? What kind of bond forms between the anion carbon
chain and sodium?

c)

Solutions
1) From left to right: Covalent, Ionic, Ionic, Covalent, Covalent, Covalent, Ionic.
2a) All products and reactants are ionic.
2b) From left to right: Covalent, Ionic, Ionic, Covalent, Ionic, Covalent, Covalent, Ionic.
2c) All products and reactants are covalent.

Further Reading

MasterOrganicChemistry
Chemical Bonding
Understanding Periodic Trends
Bond Types
Leah4Sci
Intro to Organic Chemistry 3

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Lewis Dots and the Octet Rule
Cliffs Notes
Covalent Bonding and Electronegativity
Web Pages
Counting Valence Electrons
The Octet Rule Rules!
1.2: The Octet Rule and Covalent Bonding is shared under a CC BY-NC-SA 4.0 license and was authored, remixed, and/or curated by LibreTexts.
Ionic and Covalent Bonds is licensed CC BY-NC-SA 4.0.

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1.3: Valence electrons and open valences
A valence electron is an electron that is associated with an atom, and that can participate in the formation of a chemical bond; in a
single covalent bond, both atoms in the bond contribute one valence electron in order to form a shared pair. The presence of
valence electrons can determine the element's chemical properties and whether it may bond with other elements: For a main group
element, a valence electron can only be in the outermost electron shell.
An atom with a closed shell of valence electrons (corresponding to an electron configuration s p ) tends to be chemically inert. An
2 6

atom with one or two valence electrons more than a closed shell is highly reactive, because the extra valence electrons are easily
removed to form a positive ion. An atom with one or two valence electrons fewer than a closed shell is also highly reactive,
because of a tendency either to gain the missing valence electrons (thereby forming a negative ion), or to share valence electrons
(thereby forming a covalent bond).
Like an electron in an inner shell, a valence electron has the ability to absorb or release energy in the form of a photon. An energy
gain can trigger an electron to move (jump) to an outer shell; this is known as atomic excitation. Or the electron can even break free
from its associated atom's valence shell; this is ionization to form a positive ion. When an electron loses energy (thereby causing a
photon to be emitted), then it can move to an inner shell which is not fully occupied.

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.

The periodic table of the chemical elements

Periodic table group Valence Electrons

Group 1 (I) (alkali metals) 1

Group 2 (II) (alkaline earth metals) 2

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

Group 13 (III) (boron group) 3

Group 14 (IV) (carbon group) 4

Group 15 (V) (pnictogens) 5

Group 16 (VI) (chalcogens) 6

Group 17 (VII) (halogens) 7

Group 18 (VIII or 0) (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.

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The Concept of Open Valence ("Valence")
The valence (or valency) of an element is a measure of its combining power with other atoms when it forms chemical compounds
or molecules. The concept of valence was developed in the last half of the 19th century and was successful in explaining the
molecular structure of many organic compounds. The quest for the underlying causes of valence lead to the modern theories of
chemical bonding, including Lewis structures (1916), valence bond theory (1927), molecular orbitals (1928), valence shell electron
pair repulsion theory (1958) and all the advanced methods of quantum chemistry.
The combining power or affinity of an atom of an element was determined by the number of hydrogen atoms that it combined with.
In methane, carbon has a valence of 4; in ammonia, nitrogen has a valence of 3; in water, oxygen has a valence of two; and in
hydrogen chloride, chlorine has a valence of 1. Chlorine, as it has a valence of one, can be substituted for hydrogen, so phosphorus
has a valence of 5 in phosphorus pentachloride, PCl5. Valence diagrams of a compound represent the connectivity of the elements,
lines between two elements, sometimes called bonds, represented a saturated valency for each element.[1] Examples are:-

Compoun
H2 CH4 C3H8 C2H2 NH3 NaCN H2S H2SO4 Cl2O7
d

Acetylene-
Diagram 2D.png

Sodium 1 Sulfur 6
Carbon 4 Carbon 4 Carbon 4 Sulfur 2
Hydrogen Nitrogen 3 Carbon 4 Oxygen 2 Chlorine 7
Valencies Hydrogen Hydrogen Hydrogen Hydrogen
1 Hydrogen 1 Nitrogen Hydrogen Oxygen 2
1 1 1 1
3 1

Valence only describes connectivity, it does not describe the geometry of molecular compounds, or what are now known to be ionic
compounds or giant covalent structures. The line between atoms does not represent a pair of electrons as it does in Lewis diagrams.

Further Reading

Khan Academy
Valence Electrons
Cliffs Notes
Valence Electrons
Contributors
Wikipedia

1.3: Valence electrons and open valences is shared under a CC BY-NC-SA 4.0 license and was authored, remixed, and/or curated by LibreTexts.

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1.4: Formal Charge
Chemical reactions occur via attraction and donation of electrons. Looking at the structure of a molecule can help us to understand
or to predict the behavior of that compound. One of the tools that we will eventually use to understand reactivity is formal charge.
That is because reactivity has to do with the reorganization of electrons between atoms. New chemical bonds are formed by sharing
electrons. Old chemical bonds are broken when one atom takes the bonding electrons away from another atom.
Formal charge can help us to understand the behavior of carbon monoxide, C O. When exposed to transition metal cations such as
the iron in hemoglobin (Fe2+), the carbon is attracted to and binds to the metal. In the case of hemoglobin, because the carbon
monoxide binds very strongly to the iron, the CO blocks the position where oxygen would normally be bound and carbon
monoxide poisoning results.
formal charge can help us predict how a molecule behaves
atoms with positive formal charges often attract electrons
atoms with negative formal charges often donate electrons
Why does the molecule behave in this way? There are actually a number of reasons. However, the fact that the carbon is attracted
to a metal cation begs the question: Is the carbon an anion? Yes, in a sense. In a Lewis structure of the compound, the carbon has a
formal negative charge. You will see why below.
Formal charges are an important book-keeping device that we use in Lewis structures. They tell us if one atom is donating extra
electrons to another to give it an octet. If an atom needs to donate more electrons than normal in order for everyone to get an octet,
it will have a positive formal charge. If an atom donates fewer electrons than normal and everyone still has an octet, it must be
getting extra electrons from somewhere else. It will have a negative formal charge.
formal charge is often present if the atom does not have its usual number of bonds
valence rules can act as flags to alert you that formal charges are present
To help us think about formal charges, let's look at a few small molecules that all contain carbon-oxygen multiple bonds but that
are slightly different from each other.
Example 1: Formaldehyde
Formaldehyde (CH2O) is a chemical that is used to preserve tissues; you may be familiar with its odor from anatomy lab.
Look at the structure of formaldehyde. Oxygen has a normal valence of two, and it has two bonds in formaldehyde, so there is
no formal charge on the oxygen. Carbon has a normal valence of four, and it has four bonds here. There is no formal charge on
carbon. There are no formal charges on the hydrogens either.

Example 2: Carbon Monoxide

Carbon monoxide results from burning fossil fuels; it is also an important industrial chemical used in manufacturing detergents.
Carbon monoxide has a structure that is very similar to formaldehyde. It does not have any hydrogens, though. With ten
electrons total, the only way to get an octet on both atoms is to make three bonds between carbon and oxygen.

Oxygen has normal valence two, but here it is making three bonds. It is sharing an extra pair of its electrons with carbon to
make that third bond. If it is sharing a pair of electrons, we can think of it keeping one for itself and giving the other to carbon.
Since it gives one of its electrons to carbon, it has formal charge +1.

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 Carbon has normal valence four, but here it is only making three bonds, even though it has an octet. How did it get an octet with
only three bonds? It got an extra electron from somewhere (the oxygen). It has formal charge -1.

Notice that overall the carbon monoxide molecule is neutral. Oxygen has a plus charge and carbon has a minus charge. These
charges cancel to give an overall neutral molecule.

What we are really doing when we assign formal charge is comparing how many electrons the atom brought with it from the
periodic table to how many it has now. If the atom brought four electrons of its own and it is now sharing eight, things are even. It
brought four to share and got four from its neighbors in an even trade. If it only brought three of its own and is now sharing eight, it
got more electrons than it gave, and it will have a negative charge.
To determine formal charge:
1. check the number of electrons on the atom in the periodic table
2. check the number of electrons entirely owned by the atom in the molecule; this is different than looking for an octet
3. "entirely owned" electrons include any electrons in lone pairs, since they belong completely to one atom
4. "entirely owned" electrons also include half of the electrons in the bonds to the atom, since it is sharing each of those pairs with
other atoms.
Compare the number of entirely owned valence electrons in the periodic table to those entirely owned by the atom in the molecule.
1. if the number of entirely owned electrons on the atom in the molecule is higher than in the periodic table, the atom has a
negative charge
2. if the number of entirely owned electrons on the atom in the molecule is lower than in the periodic table, the atom has a positive
charge
3. the formal charge is additive: if the atom has two extra electrons in the molecule, it has a two minus charge. If it is two short, it
has a two plus charge.
Remember, electron counting to determine an octet counts all of the bonding and nonbonding electrons equally. It is done simply to
determine whether the atom has a noble gas configuration right now. Electron counting to determine formal charge is done to keep
track of who has given electrons to whom when making the molecule. If, in getting to an octet, atoms have received more electrons
than they have given, their electron/proton ratio has changed, and they become charged.
Example 3: Carbonate Ion
Calcium carbonate is found in limestone and chalk, for instance.

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Problem IM5.1
Draw Lewis or Kekule structures for the following molecules, remembering to include formal charges, if any (and notice that some
of these molecules are ions):
a. NO+
b. CN-
c. CH3O-
d. CH3+
e. HNO3
f. CH3CO2-

Problem IM5.2.
Given the structures below, assign any missing formal charges.

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Problem IM5.3.
Given the structures below, draw in the missing electrons, if any.

Contributors
Chris P Schaller, Ph.D., (College of Saint Benedict / Saint John's University)

Further Reading

MasterOrganicChemistry
How to Calculate Formal Charge
Common Mistakes: Formal Charge Can Mislead

Khan Academy
Formal Charge I
Formal Charge II

Carey 4th Ed Online

Lewis Structures and Formal Charge

Web Pages
Formal Charge Tutorial (with problems)
Videos

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Formal Charge
Berkeley Video on Formal Charge
Formal Charge Video
Tutorial
How To Determine Formal Charges
1.4: Formal Charge is shared under a CC BY-NC-SA 4.0 license and was authored, remixed, and/or curated by LibreTexts.

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1.5: Resonance
Resonance is a mental exercise within the Valence Bond Theory of bonding that describes the delocalization of electrons within
molecules. It involves constructing multiple Lewis structures that, when combined, represent the full electronic structure of the
molecule. Resonance structures are used when a single Lewis structure cannot fully describe the bonding; the combination of
possible resonance structures is defined as a resonance hybrid, which represents the overall delocalization of electrons within the
molecule. In general, molecules with multiple resonance structures will be more stable than one with fewer and some resonance
structures contribute more to the stability of the molecule than others - formal charges aid in determining this.

Introduction
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 resonance
structures. The nuclear skeleton of the Lewis Structure of these resonance structures remains the same, only the electron locations
differ. Such is the case for ozone (O ), an allotrope of oxygen with a V-shaped structure and an O–O–O angle of 117.5°. Let's
3

motivate the discussion by building the Lewis structure for ozone.

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

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

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

with 14 electrons left over.

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

and have 2 electrons left over.

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

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

Which is correct? In fact, neither is correct. Both predict one O–O single bond and one O=O double bond. As you will learn, 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:

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The double-headed arrow indicates that the actual electronic structure is an average of those shown, not that the molecule oscillates
between the two structures.

When it is possible to write more than one equivalent resonance structure for a molecule
or ion, the actual structure is the average of the resonance structures.
The electrons appear to "shift" between different resonance structures and while not strictly correct as each resonance structure is
just a limitation of using the Lewis structure perspective to describe these molecules. A more accurate description of the electron
structure of the molecule requires considering multiple resonance structures simultaneously.

 Delocalization and Resonance Structures Rules

1. Resonance structures should have the same number of electrons, do not add or subtract any electrons. (check the number of
electrons by simply counting them).
2. Each resonance structures follows the rules of writing Lewis Structures.
3. The hybridization of the structure must stay the same.
4. The skeleton of the structure can not be changed (only the electrons move).
5. Resonance structures must also have the same number of lone pairs.

 "Pick the Correct Arrow for the Job"

Most arrows in chemistry cannot be used interchangeably and care must be given to selecting the correct arrow for the job.
↔: A double headed arrow on both ends of the arrow between Lewis structures is used to show resonance
⇌: Double harpoons are used to designate equilibria
⇀: A single harpoon on one end indicates the movement of one electron

→: A double headed arrow on one end is used to indicate the movement of two electrons

 Example 1.5.2: Carbonate Ion

Identify the resonance structures for the carbonate ion: CO 2 −

3
.

Solution
1. Because carbon is the least electronegative element, we place it in the central position:

2. Carbon has 4 valence electrons, each oxygen has 6 valence electrons, and there are 2 more for the −2 charge. This gives 4 + (3 ×
6) + 2 = 24 valence electrons.
3. Six electrons are used to form three bonding pairs between the oxygen atoms and the carbon:

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

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

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

The actual structure is an average of these three resonance structures.

Like ozone, the electronic structure of the carbonate ion cannot be described by a single Lewis electron structure. Unlike O3,
though, the actual structure of CO32− is an average of three resonance structures.

Using Formal Charges to Identify viable Resonance Structures

While each resonance structure contributes to the total electronic structure of the molecule, they may not contribute equally.
Assigning Formal charges to atoms in the molecules is one mechanism to identify the viability of a resonance structure and
determine its relative magnitude among other structures. The formal charge on an atom in a covalent species is the net charge the
atom would bear if the electrons in all the bonds to the atom were equally shared. Alternatively the formal charge on an atom in a
covalent species is the net charge the atom would bear if all bonds to the atom were nonpolar covalent bonds. To determine the
formal charge on a given atom in a covalent species, use the following formula:
Formal Charge = (number of valence electrons in free orbital) − (number of lone-pair electrons) (1.5.1)

1
− ( number bond pair electrons)
2

 Rules for estimating stability of resonance structures

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

 Example 1.5.3: Thiocyanate Ion

Consider the thiocyanate (C N S ) ion.

−

Solution
1. Find the Lewis Structure of the molecule. (Remember the Lewis Structure rules.)

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

3. Assign Formal Charges via Equation 1.5.1.

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

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

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

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

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

It is useful to combine the resonance structures into a single structure called the Resonance Hybrid that describes the bonding of
the molecule. The general approach is described below:
1. Draw the Lewis Structure & Resonance for the molecule (using solid lines for bonds).

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 2. Where there can be a double or triple bond, draw a dotted line (-----) for the bond.
3. Draw only the lone pairs found in all resonance structures, do not include the lone pairs that are not on all of the resonance
structures.

 Example 1.5.4: Benzene

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 (C H ) consists of a regular hexagon of carbon atoms,
6 6

each of which is also bonded to a hydrogen atom. Use resonance structures to describe the bonding in benzene.
Given: molecular formula and molecular geometry
Asked for: resonance structures
Strategy:
A. Draw a structure for benzene illustrating the bonded atoms. Then calculate the number of valence electrons used in this
drawing.
B. Subtract this number from the total number of valence electrons in benzene and then locate the remaining electrons such
that each atom in the structure reaches an octet.
C. Draw the resonance structures for benzene.
Solution:
A Each hydrogen atom contributes 1 valence electron, and each carbon atom contributes 4 valence electrons, for a total of (6 ×
1) + (6 × 4) = 30 valence electrons. If we place a single bonding electron pair between each pair of carbon atoms and between
each carbon and a hydrogen atom, we obtain the following:

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

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

Each structure has alternating double and single bonds, but experimentation shows that each carbon–carbon bond in benzene is
identical, with bond lengths (139.9 pm) intermediate between those typically found for a C–C single bond (154 pm) and a C=C
double bond (134 pm). We can describe the bonding in benzene using the two resonance structures, but the actual electronic

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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:

 Example 1.5.5: Nitrate Ion

Draw the possible resonance structures for the Nitrate ion NO . −

Solution
1. Count up the valence electrons: (1*5) + (3*6) + 1(ion) = 24 electrons
2. Draw the bond connectivities:

3. Add octet electrons to the atoms bonded to the center atom:

4. Place any leftover electrons (24-24 = 0) on the center atom:

5. Does the central atom have an octet?

NO, it has 6 electrons
Add a multiple bond (first try a double bond) to see if the central atom can achieve an octet:

6. Does the central atom have an octet?

YES
Are there possible resonance structures? YES

Note: We would expect that the bond lengths in the NO ion to be somewhat shorter than a single bond.
−

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References
1. Petrucci, Ralph H., et al. General Chemistry: Principles and Modern Applications. New Jersey: Pearson Prentice Hall, 2007.
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.

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-.

Problems #2

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

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

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

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

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

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

Problems #2

Contributors and Attributions

Sharon Wei (UCD), Liza Chu (UCD)

Further Reading

MasterOrganicChemistry
Introduction to Resonance part 1
Introduction to Resonance part 2
Evaluating Resonance Forms 1 – the Rule of Least Charges
Evaluating Resonance Forms 2 – applying electronegativity
Evaluating Resonance Forms 3 – Negative Charges
Evaluating Resonance Forms 4 – Positive Charges

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Exploring Resonance 1 – Pi Donation
Applying Resonance 2 – Pi Acceptors
In Summary – Resonance
Common Mistakes – How Not To Draw Resonance Curved Arrows

Carey 4th Edition On-Line Activity

Resonance
Khan Academy
Formal Charge and Resonace Part 1
Formal Charge and Resonance Part 2

Leah4Sci
Electron Pushing Arrows in Resonance and Organic Mechanisms
Cliffs Notes
Slide Presentations
Web Pages
Lewis Structures, Isomers, Resonance
Lewis Structures, Formal Charge and Resonance
More About Resonance
Resonance Structures and Arrows
Another Resonance Page
Difference between isomers and Resonance Structures
Some Resonance Structure Info
Useful Info On Curved Arrows

Videos
Series of Resonance Structure Videos
Resonance Structure Video

Tutorial

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Assessing resonance structures
Guide to Assessing Resonance Structures
1.5: Resonance is shared under a CC BY-NC-SA 4.0 license and was authored, remixed, and/or curated by LibreTexts.
Resonance is licensed CC BY-NC-SA 4.0.

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1.6: Electronegativity and Bond Polarization
Electronegativity is a measure of the tendency of an atom to attract a bonding pair of electrons. The Pauling scale is the most
commonly used. Fluorine (the most electronegative element) is assigned a value of 4.0, and values range down to cesium and
francium which are the least electronegative at 0.7.

What if two atoms of equal electronegativity bond together?

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

To get a bond like this, A and B would usually have to be the same atom. You will find this sort of bond in, for example, H2 or Cl2
molecules. Note: It's important to realize that this is an average picture. The electrons are actually in a molecular orbital, and are
moving around all the time within that orbital. This sort of bond could be thought of as being a "pure" covalent bond - where the
electrons are shared evenly between the two atoms.

What if B is slightly more electronegative than A?

B will attract the electron pair rather more than A does.

That means that the B end of the bond has more than its fair share of electron density and so becomes slightly negative. At the same
time, the A end (rather short of electrons) becomes slightly positive. In the diagram, "δ " (read as "delta") means "slightly" - so δ+
means "slightly positive".
A polar bond is a covalent bond in which there is a separation of charge between one end and the other - in other words in which
one end is slightly positive and the other slightly negative. Examples include most covalent bonds. The hydrogen-chlorine bond in
HCl or the hydrogen-oxygen bonds in water are typical.

If B is a lot more electronegative than A, then the electron pair is dragged right over to B's end of the bond. To all intents and
purposes, A has lost control of its electron, and B has complete control over both electrons. Ions have been formed. The bond is
then an ionic bond rather than a covalent bond.

A "spectrum" of bonds
The implication of all this is that there is no clear-cut division between covalent and ionic bonds. In a pure 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.

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

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  Example 1: Polar Bonds vs. Polar Molecules

In a simple diatomic molecule like HCl, if the bond is polar, then the whole molecule is polar. What about more complicated
molecules?

Figure 1.6.1 : (left) CCl4 (right) CHCl3

Consider CCl4, (left panel in figure above), which as a molecule is not polar - in the sense that it doesn't have an end (or a side)
which is slightly negative and one which is slightly positive. The whole of the outside of the molecule is somewhat negative,
but there is no overall separation of charge from top to bottom, or from left to right.
In contrast, CHCl3 is a polar molecule (right panel in figure above). 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.
A polar molecule will need to be "lop-sided" in some way.

Patterns of electronegativity in the Periodic Table

The distance of the electrons from the nucleus remains relatively constant in a periodic table row, but not in a periodic table
column. The force between two charges is given by Coulomb’s law.
Q1 Q2
F =k (1.6.1)
2
r

In this expression, Q represents a charge, k represents a constant and r is the distance between the charges. When r = 2, then r2= 4.
When r = 3, then r2 = 9. When r = 4, then r2 = 16. It is readily seen from these numbers that, as the distance between the charges
increases, the force decreases very rapidly. This is called a quadratic change.
The result of this change is that electronegativity increases from bottom to top in a column in the periodic table even though there
are more protons in the elements at the bottom of the column. Elements at the top of a column have greater electronegativities than
elements at the bottom of a given column.
The overall trend for electronegativity in the periodic table is diagonal from the lower left corner to the upper right corner. Since
the electronegativity of some of the important elements cannot be determined by these trends (they lie in the wrong diagonal), we
have to memorize the following order of electronegativity for some of these common elements.
F > O > Cl > N > Br > I > S > C > H > metals
The most electronegative element is fluorine. If you remember that fact, everything becomes easy, because electronegativity must
always increase towards fluorine in the Periodic Table.

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  Note

This simplification ignores the noble gases. Historically this is because they were believed not to form bonds - and if they do
not form bonds, they cannot have an electronegativity value. Even now that we know that some of them do form bonds, data
sources still do not quote electronegativity values for them.

Trends in electronegativity across a period

The positively charged protons in the nucleus attract the negatively charged electrons. As the number of protons in the nucleus
increases, the electronegativity or attraction will increase. Therefore electronegativity increases from left to right in a row in the
periodic table. This effect only holds true for a row in the periodic table because the attraction between charges falls off rapidly
with distance. The chart shows electronegativities from sodium to chlorine (ignoring argon since it does not does not form bonds).

Trends in electronegativity down a group

As you go down a group, electronegativity decreases. (If it increases up to fluorine, it must decrease as you go down.) The chart
shows the patterns of electronegativity in Groups 1 and 7.

Explaining the patterns in electronegativity

The attraction that a bonding pair of electrons feels for a particular nucleus depends on:
the number of protons in the nucleus;
the distance from the nucleus;
the amount of screening by inner electrons.

Why does electronegativity increase across a period?

Consider sodium at the beginning of period 3 and chlorine at the end (ignoring the noble gas, argon). Think of sodium chloride as if
it were covalently bonded.

Both sodium and chlorine have their bonding electrons in the 3-level. The electron pair is screened from both nuclei by the 1s, 2s
and 2p electrons, but the chlorine nucleus has 6 more protons in it. It is no wonder the electron pair gets dragged so far towards the
chlorine that ions are formed. Electronegativity increases across a period because the number of charges on the nucleus increases.
That attracts the bonding pair of electrons more strongly.

Why does electronegativity fall as you go down a group?

As you go down a group, electronegativity decreases because the bonding pair of electrons is increasingly distant from the
attraction of the nucleus. Consider the hydrogen fluoride and hydrogen chloride molecules:

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The bonding pair is shielded from the fluorine's nucleus only by the 1s2 electrons. In the chlorine case it is shielded by all the
1s22s22p6 electrons. In each case there is a net pull from the center of the fluorine or chlorine of +7. But fluorine has the bonding
pair in the 2-level rather than the 3-level as it is in chlorine. If it is closer to the nucleus, the attraction is greater.

Diagonal relationships in the Periodic Table

At the beginning of periods 2 and 3 of the Periodic Table, there are several cases where an element at the top of one group has
some similarities with an element in the next group. Three examples are shown in the diagram below. Notice that the similarities
occur in elements which are diagonal to each other - not side-by-side.

For example, boron is a non-metal with some properties rather like silicon. Unlike the rest of Group 2, beryllium has some
properties resembling aluminum. And lithium has some properties which differ from the other elements in Group 1, and in some
ways resembles magnesium. There is said to be a diagonal relationship between these elements. There are several reasons for this,
but each depends on the way atomic properties like electronegativity vary around the Periodic Table. So we will have a quick look
at this with regard to electronegativity - which is probably the simplest to explain.

Explaining the diagonal relationship with regard to electronegativity

Electronegativity increases across the Periodic Table. So, for example, the electronegativities of beryllium and boron are:

Be 1.5

B 2.0

Electronegativity falls as you go down the Periodic Table. So, for example, the electronegativities of boron and aluminum are:

B 2.0

Al 1.5

So, comparing Be and Al, you find the values are (by chance) exactly the same. The increase from Group 2 to Group 3 is offset by
the fall as you go down Group 3 from boron to aluminum. Something similar happens from lithium (1.0) to magnesium (1.2), and
from boron (2.0) to silicon (1.8). In these cases, the electronegativities are not exactly the same, but are very close.
Similar electronegativities between the members of these diagonal pairs means that they are likely to form similar types of bonds,
and that will affect their chemistry. You may well come across examples of this later on in your course.

Further Reading

Khan Academy
Electronegativity and Bond Polarity

Cliffs Notes
Covalent Bonding and Electronegativity
Videos
Polar bonds and Electronegativity
1.6: Electronegativity and Bond Polarization is shared under a CC BY-NC-SA 4.0 license and was authored, remixed, and/or curated by
LibreTexts.

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Electronegativity by Jim Clark is licensed CC BY-NC 4.0.

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1.7: Atomic Orbitals and Covalent Bonding
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?
Valence bond theory is most often used to describe bonding in organic molecules. In this
model, bonds are considered to form from the overlap of two atomic orbitals on different atoms,
each orbital containing a single electron. In looking at simple inorganic molecules such as
molecular hydrogen (H2) or hydrogen fluoride (HF), our present understanding of s and p
atomic orbitals will suffice. In order to explain the bonding in organic molecules, however, we
will need to introduce the concept of hybrid orbitals.

The sigma bond in the H2 molecule

The simplest case to consider is the hydrogen molecule, H2. When we say that the two hydrogen nuclei share their
electrons to form a covalent bond, what we mean in valence bond theory terms is that the two spherical 1s orbitals (the
grey spheres in the figure below) overlap, and contain two electrons with opposite spin.

These two electrons are now attracted to the positive charge of both of the hydrogen nuclei, with the result that they
serve as a sort of ‘chemical glue’ holding the two nuclei together.
How far apart are the two nuclei? If they are too far apart, their respective 1s orbitals cannot overlap, and thus no
covalent bond can form - they are still just two separate hydrogen atoms. As they move closer and closer together,
orbital overlap begins to occur, and a bond begins to form. This lowers the potential energy of the system, as new,
attractive positive-negative electrostatic interactions become possible between the nucleus of one atom and the
electron of the second.
But something else is happening at the same time: as the atoms get closer, the repulsive positive-positive interaction
between the two nuclei also begins to increase.

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At first this repulsion is more than offset by the attraction between nuclei and electrons, but at a certain point, as the
nuclei get even closer, the repulsive forces begin to overcome the attractive forces, and the potential energy of the
system rises quickly. When the two nuclei are ‘too close’, we have an unstable, high-energy situation. There is a
defined optimal distance between the nuclei in which the potential energy is at a minimum, meaning that the combined
attractive and repulsive forces add up to the greatest overall attractive force. 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 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.
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.
Table of bond lengths and bond energies
It is not accurate, however, to picture covalent bonds as rigid sticks of unchanging length - rather, it is better to picture
them as springs which have a defined length when relaxed, but which can be compressed, extended, and bent. This
‘springy’ picture of covalent bonds will become very important in chapter 4, when we study the analytical technique
known as infrared (IR) spectroscopy.
One 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.

A sigma bond can be formed by overlap of an s atomic orbital with a p atomic orbital. Hydrogen
fluoride (HF) is an example:

A sigma bond can also be formed by the overlap of two p orbitals. The covalent bond in molecular fluorine, F2, is a
sigma bond formed by the overlap of two half-filled 2p orbitals, one from each fluorine atom.

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sp3 hybrid orbitals and tetrahedral bonding
Now let’s look more carefully at bonding in organic molecules, starting with methane, CH4. Recall the valence electron
configuration of a carbon atom:

This picture is problematic when it comes to describing the bonding in methane. How does the carbon form four bonds
if it has only two half-filled p orbitals available for bonding? A hint comes from the experimental observation that the
four C-H bonds in methane are arranged with tetrahedral geometry about the central carbon, and that each bond has
the same length and strength. 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 wave equations) to form four equivalent hybrid orbitals, which
are called 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.

interactive 3D model
(select 'load sp3' and 'load H 1s' to see orbitals)
This geometric arrangement makes perfect sense if you consider that it is precisely this angle that allows the four
orbitals (and the electrons in them) to be as far apart from each other as possible. This is simply a restatement of the
Valence Shell Electron Pair Repulsion (VSEPR) theory that you learned in General Chemistry: electron pairs (in
orbitals) will arrange themselves in such a way as to remain as far apart as possible, due to negative-negative
electrostatic repulsion.
Each C-H bond in methane, then, can be described as a sigma bond formed by overlap between a half-filled 1s orbital
in a hydrogen atom and the larger lobe of one of the four half-filled sp3 hybrid orbitals in the central carbon. The length
of the carbon-hydrogen bonds in methane is 109 pm.

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While previously we drew a Lewis structure of methane in two dimensions using lines to denote each covalent bond,
we can now draw a more accurate structure in three dimensions, showing the tetrahedral bonding geometry. To do this
on a two-dimensional page, though, we need to introduce a new drawing convention: the solid / dashed wedge system.
In this convention, a solid wedge simply represents a bond that is meant to be pictured emerging from the plane of the
page. A dashed wedge represents a bond that is meant to be pictured pointing into, or behind, the plane of the page.
Normal lines imply bonds that lie in the plane of the page. This system takes a little bit of getting used to, but with
practice your eye will learn to immediately ‘see’ the third dimension being depicted.

Exercise 2.1: Imagine that you could distinguish between the four hydrogen atoms in a methane molecule, and
labeled them Ha through Hd. In the images below, the exact same methane molecule is rotated and flipped in
various positions. Draw the missing hydrogen atom labels. (It will be much easier to do this if you make a model.)

Exercise 2.2: What kind of orbitals overlap to form the C-Cl bonds in chloroform, CHCl3?
Solutions to exercises

How does this bonding picture extend to compounds containing carbon-carbon bonds? In ethane (CH3CH3), both
carbons are sp3-hybridized, meaning that both have four bonds with tetrahedral geometry. The carbon-carbon bond,
with a bond length of 154 pm, is formed by overlap of one sp3 orbital from each of the carbons, while the six carbon-
hydrogen bonds are formed from overlaps between the remaining sp3 orbitals on the two carbons and the 1s orbitals of
hydrogen atoms. All of these are sigma bonds.

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

In chapter 3 we will learn more about the implications of rotational freedom in sigma bonds, when we discuss the
‘conformation’ of organic molecules.
The sp3 bonding picture is also used to described the bonding in amines, including ammonia, the simplest amine. Just
like the carbon atom in methane, the central nitrogen in ammonia is sp3-hybridized. With nitrogen, however, there are

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five rather than four valence electrons to account for, meaning that three of the four hybrid orbitals are half-filled and
available for bonding, while the fourth is fully occupied by a nonbonding pair (lone pair) of electrons.

space-filling image
The bonding arrangement here is also tetrahedral: the three N-H bonds of ammonia can be pictured as forming the
base of a trigonal pyramid, with the fourth orbital, containing the lone pair, forming the top of the pyramid. Recall from
your study of VSEPR theory in General Chemistry that the lone pair, with its slightly greater repulsive effect, ‘pushes’
the three N-H s bonds away from the top of the pyramid, meaning that the H-N-H bond angles are slightly less than
tetrahedral, at 107.3˚ rather than 109.5˚.
VSEPR theory also predicts, accurately, that a water molecule is ‘bent’ at an angle of approximately 104.5˚. The
bonding in water results from overlap of two of the four sp3 hybrid orbitals on oxygen with 1s orbitals on the two
hydrogen atoms. The two nonbonding electron pairs on oxygen are located in the two remaining sp3 orbitals.

Exercise 2.3: Draw,

in the same style as the figures above, orbital pictures for the bonding in a)
methylamine, and b) ethanol.
Solutions to exercises

video tutorial on sp3 orbitals and sigma bonds

sp2 and sp hybrid orbitals and pi bonds

The valence bond theory, along with the hybrid orbital concept, does a very good job of describing double-bonded
compounds such as ethene. Three experimentally observable characteristics of the ethene molecule need to be
accounted for by a bonding model:
1. Ethene is a planar (flat) molecule.

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2. Bond angles in ethene are approximately 120o, and the carbon-carbon bond length is 134 pm, significantly shorter
than the 154 pm single carbon-carbon bond in ethane.
3. There is a significant barrier to rotation about the carbon-carbon double bond.

Clearly, these characteristics are not consistent with an sp3 hybrid bonding picture for the two carbon atoms. Instead,
the bonding in ethene is described by a model involving the participation of a different kind of hybrid orbital. Three
atomic orbitals on each carbon – the 2s, 2px and 2py orbitals – combine to form three sp2 hybrids, leaving the 2pz
orbital unhybridized.

The three sp2 hybrids are arranged with trigonal planar geometry, pointing to the three corners of an equilateral
triangle, with angles of 120° between them. The unhybridized 2pz orbital is perpendicular to this plane (in the next
several figures, sp2 orbitals and the sigma bonds to which they contribute are represented by lines and wedges; only
the 2pz orbitals are shown in the 'space-filling' mode).

The carbon-carbon double bond in ethene consists of one sigma bond, formed by the overlap of two sp2 orbitals, and a
second bond, called a pi bond, which is formed by the side-by-side overlap of the two unhybridized 2pz orbitals from
each carbon.

animation spacefilling image video tutorial interactive 3D model (select 'show resulting pi orbital')
Unlike a sigma bond, a pi bond does not have cylindrical symmetry. 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. The presence of the
pi bond thus ‘locks’ the six atoms of ethene into the same plane. This argument extends to larger alkene groups: in
each case, six atoms lie in the same plane.

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 Exercise 2.4:
Redraw the structures below, indicating the six atoms that lie in the same plane
due to the carbon-carbon double bond.

Exercise 2.5: What is wrong with the way the following structure is drawn?

Solutions to exercises

A similar picture can be drawn for the bonding in carbonyl groups, such as formaldehyde. In this molecule, the carbon
is sp2-hybridized, and we will assume that the oxygen atom is also sp2 hybridized. The carbon has three sigma bonds:
two are formed by overlap between sp2 orbitals with 1s orbitals from hydrogen atoms, and the third sigma bond is
formed by overlap between the remaining carbon sp2 orbital and an sp2 orbital on the oxygen. The two lone pairs on
oxygen occupy its other two sp2 orbitals.

interactive 3D model
The pi bond is formed by side-by-side overlap of the unhybridized 2pz orbitals on the carbon and the oxygen. Just like
in alkenes, the 2pz orbitals that form the pi bond are perpendicular to the plane formed by the sigma bonds.
Exercise 2.6:
a: Draw a diagram of hybrid orbitals in an sp2-hybridized nitrogen.
b: Draw a figure showing the bonding picture for the imine below.

c: In your drawing for part b, what kind of orbital holds the nitrogen lone pair?
Solutions to exercises

Recall that carbocations are transient, high-energy species in which a carbon only has three bonds (rather than the
usual four) and a positive formal charge. We will have much more to say about carbocations in this and later chapters.

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For now, though, the important thing to understand is that a carbocation can be described as an sp2-hybridized carbon
with an empty p orbital perpendicular to the plane of the sigma bonds.

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

Both the VSEPR theory and experimental evidence tells us that the molecule is linear: all four
atoms lie in a straight line. The carbon-carbon triple bond is only 120 pm long, shorter than the
double bond in ethene, and is very strong, about 837 kJ/mol. 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 unhybridized,
and are oriented perpendicularly along the y and z axes, respectively.

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

space-filling image
interactive 3D model

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 Exercise 2.7:
Look at the structure of thiamine diphosphate in the 'structures of common
coenzymes' table. Identify the hybridization of all carbon atoms in the molecule.
Solutions to exercises

The hybrid orbital concept nicely explains another experimental observation: single bonds adjacent to double and triple
bonds are progressively shorter and stronger than single bonds adjacent to other single bonds. Consider for example,
the carbon-carbon single bonds in propane, propene, and propyne.

All three are single (sigma) bonds; the bond in propyne is shortest and strongest, while the
bond in propane is longest and weakest. The explanation 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. It follows that electrons in an sp orbital, with its greater s character, are closer to the
nucleus than electrons in an sp2 or sp3 orbital. Consequently, bonds involving sp-sp3 overlap
(as in propyne) are shorter and stronger than bonds involving sp2-sp3 overlap (as in propene).
Bonds involving sp3-sp3 overlap (as in propane) are the longest and weakest of the three.

Exercise 2.8:
a) What kinds of orbitals are overlapping in bonds b-i indicated below? Be sure to distinguish between s and p
bonds. An example is provided for bond 'a'.
b) In what kind of orbital is the lone pair of electrons located on the nitrogen atom of bond a? Of bond e?

Solutions to exercises

Kahn Academy video tutorial on valence bond theory / hybrid orbitals

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

Further Reading

Khan Academy
Sigma Bonds and sp3 Orbitals
Pi Bonding and sp2 Orbitals

Leah4Sci
Drawing Skeletal Structures of Bond-Line Notations of Organic Molecules

Web Pages
Sigma Bonds
Pi Bonds
Sigma and Pi Bonds
Videos
Sigma and Pi Bonds
Sigma and Pi Bonds
1.7: Atomic Orbitals and Covalent Bonding is shared under a CC BY-NC-SA 4.0 license and was authored, remixed, and/or curated by
LibreTexts.

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1.8: Hybridization
Hybridization was introduced to explain molecular structure when the valence bond theory failed to correctly predict them. It is
experimentally observed that bond angles in organic compounds are close to 109o, 120o, or 180o. According to Valence Shell
Electron Pair Repulsion (VSEPR) theory, electron pairs repel each other and the bonds and lone pairs around a central atom are
generally separated by the largest possible angles.

Introduction
Carbon is a perfect example showing the value of hybrid orbitals. Carbon's ground state configuration is:

According to Valence Bond Theory, carbon should form two covalent bonds, resulting in a CH2, because it has two unpaired
electrons in its electronic configuration.However, experiments have shown that C H is highly reactive and cannot exist outside of
2

a reaction. Therefore, this does not explain how CH4 can exist. To form four bonds the configuration of carbon must have four
unpaired electrons.
One way CH4 can be explained is, the 2s and the 3 2p orbitals combine to make four, equal energy sp3 hybrid orbitals. That would
give us the following configuration:

Now that carbon has four unpaired electrons it can have four equal energy bonds. The hybridization of orbitals is favored because
hybridized orbitals are more directional which leads to greater overlap when forming bonds, therefore the bonds formed are
stronger. This results in more stable compounds when hybridization occurs.
The next section will explain the various types of hybridization and how each type helps explain the structure of certain molecules.

sp3 hybridization
sp3 hybridization can explain the tetrahedral structure of molecules. In it, the 2s orbitals and all three of the 2p orbitals hybridize to
form four sp3 orbitals, each consisting of 75% p character and 25% s character. The frontal lobes align themselves in the manner
shown below. In this structure, electron repulsion is minimized.
Energy changes occurring in hybridization

Hybridization of an s orbital with all three p orbitals (px , py, and pz) results in four sp3 hybrid orbitals. sp3 hybrid orbitals are
oriented at bond angle of 109.5o from each other. This 109.5o arrangement gives tetrahedral geometry (Figure 4).

Example: sp3 Hybridization in Methane

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 Because carbon plays such a significant role in organic chemistry, we will be using it as an example here. Carbon's 2s and all three of its 2p
orbitals hybridize to form four sp3 orbitals. These orbitals then bond with four hydrogen atoms through sp3-s orbital overlap, creating methane.
The resulting shape is tetrahedral, since that minimizes electron repulsion.
Hybridization

Lone Pairs: Remember to take into account lone pairs of electrons. These lone pairs cannot double bond so they are placed in their own hybrid
orbital. This is why H2O is tetrahedral. We can also build sp3d and sp3d2 hybrid orbitals if we go beyond s and p subshells.

sp2 hybridization
sp2 hybridization can explain the trigonal planar structure of molecules. In it, the 2s orbitals and two of the 2p orbitals hybridize to
form three sp orbitals, each consisting of 67% p and 33% s character. The frontal lobes align themselves in the trigonal planar
structure, pointing to the corners of a triangle in order to minimize electron repulsion and to improve overlap. The remaining p
orbital remains unchanged and is perpendicular to the plane of the three sp2 orbitals.

Energy changes occurring in hybridization

Hybridization of an s orbital with two p orbitals (px and py) results in three sp2 hybrid orbitals that are oriented at 120o angle to
each other (Figure 3). Sp2 hybridization results in trigonal geometry.
figure3.gif

Example: sp2 Hybridization in Aluminum Trihydride

In aluminum trihydride, one 2s orbital and two 2p orbitals hybridize to form three sp2 orbitals that align themselves in the trigonal planar structure.
The three Al sp2 orbitals bond with with 1s orbitals from the three hydrogens through sp2-s orbital overlap.

Example: sp2 Hybridization in Ethene

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 Similar hybridization occurs in each carbon of ethene. For each carbon, one 2s orbital and two 2p orbitals hybridize to form three sp2 orbitals.
These hybridized orbitals align themselves in the trigonal planar structure. For each carbon, two of these sp orbitals bond with two 1s hydrogen
orbitals through s-sp orbital overlap. The remaining sp2 orbitals on each carbon are bonded with each other, forming a bond between each carbon
through sp2-sp2 orbital overlap. This leaves us with the two p orbitals on each carbon that have a single carbon in them. These orbitals form a ?
bonds through p-p orbital overlap, creating a double bond between the two carbons. Because a double bond was created, the overall structure of
the ethene compound is linear. However, the structure of each molecule in ethene, the two carbons, is still trigonal planar.

sp Hybridization
sp Hybridization can explain the linear structure in molecules. In it, the 2s orbital and one of the 2p orbitals hybridize to form two
sp orbitals, each consisting of 50% s and 50% p character. The front lobes face away from each other and form a straight line
leaving a 180° angle between the two orbitals. This formation minimizes electron repulsion. Because only one p orbital was used,
we are left with two unaltered 2p orbitals that the atom can use. These p orbitals are at right angles to one another and to the line
formed by the two sp orbitals.
Energy changes occurring in hybridization

Figure 1: Notice how the energy of the electrons lowers when hybridized.
These p orbitals come into play in compounds such as ethyne where they form two addition? bonds, resulting in in a triple bond.
This only happens when two atoms, such as two carbons, both have two p orbitals that each contain an electron. An sp hybrid
orbital results when an s orbital is combined with p orbital (Figure 2). We will get two sp hybrid orbitals since we started with two
orbitals (s and p). sp hybridization results in a pair of directional sp hybrid orbitals pointed in opposite directions. These hybridized
orbitals result in higher electron density in the bonding region for a sigma bond toward the left of the atom and for another sigma
bond toward the right. In addition, sp hybridization provides linear geometry with a bond angle of 180o.

Example: sp Hybridization in Magnesium Hydride

In magnesium hydride, the 3s orbital and one of the 3p orbitals from magnesium hybridize to form two sp orbitals. The two frontal lobes of the sp
orbitals face away from each other forming a straight line leading to a linear structure. These two sp orbitals bond with the two 1s orbitals of the
two hydrogen atoms through sp-s orbital overlap.
Hybridization

Example: sp Hybridization in Ethyne

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 The hybridization in ethyne is similar to the hybridization in magnesium hydride. For each carbon, the 2s orbital hybridizes with one of the 2p
orbitals to form two sp hybridized orbitals. The frontal lobes of these orbitals face away from each other forming a straight line. The first bond
consists of sp-sp orbital overlap between the two carbons. Another two bonds consist of s-sp orbital overlap between the sp hybridized orbitals of
the carbons and the 1s orbitals of the hydrogens. This leaves us with two p orbitals on each carbon that have a single carbon in them. This allows
for the formation of two ? bonds through p-p orbital overlap. The linear shape, or 180° angle, is formed because electron repulsion is minimized
the greatest in this position.
Hybridization

References
1. John Olmsted, Gregory M. Williams Chemistry: The Molecular Science Jones & Bartlett Publishers 1996. 366-371
2. Francis A. Carey Advanced Organic Chemistry Springer 2001. 4-6
3. L. G. Wade, Jr. Whitman College Organic Chemistry Fifth Edition 2003

Problems
Using the Lewis Structures, try to figure out the hybridization (sp, sp2, sp3) of the indicated atom and indicate the atom's shape.
1. The carbon.

2. The oxygen.

3. The carbon on the right.

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Answers
1. sp2- Trigonal Planar
The carbon has no lone pairs and is bonded to three hydrogens so we just need three hybrid orbitals, aka sp2.
2. sp3 - Tetrahedral
Don't forget to take into account all the lone pairs. Every lone pair needs it own hybrid orbital. That makes three hybrid
orbitals for lone pairs and the oxygen is bonded to one hydrogen which requires another sp3 orbital. That makes 4 orbitals,
aka sp3.
3. sp - Linear
The carbon is bonded to two other atoms, that means it needs two hybrid orbitals, aka sp.
An easy way to figure out what hybridization an atom has is to just count the number of atoms bonded to it and the number of lone
pairs. Double and triple bonds still count as being only bonded to one atom. Use this method to go over the above problems again
and make sure you understand it. It's a lot easier to figure out the hybridization this way.

Contributors
Harpreet Chima (UCD), Farah Yasmeen

Further Reading

Carey 4th Edition On-Line Activity

Hybridization
Web Pages
Hybrid Orbitals
Hybrid Orbitals
Valence Bond Theory and Hybrid Orbitals
Hybridization of Carbon
Videos
Hybrid Orbitals
Hybridization
Hybridization
1.8: Hybridization is shared under a CC BY-NC-SA 4.0 license and was authored, remixed, and/or curated by LibreTexts.
Hybrid Orbitals is licensed CC BY-NC-SA 4.0.

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1.9: Representation of Molecular Structure
Chemistry is the experimental and theoretical study of materials on their properties at both the macroscopic and microscopic levels.
Understanding the relationship between properties and structures/bonding is also a hot pursuit. Chemistry is traditionally divided
into organic and inorganic chemistry. The former is the study of compounds containing at least one carbon-hydrogen bonds. By
default, the chemical study of all other substances is called inorganic chemistry, a less well defined subject.
However, the boundary between organic and inorganic compounds is not always well defined. For example, oxalic acid, H2C2O4, is
a compound formed in plants, and it is generally considered an organic acid, but it does not contain any C-H bond. Inorganic
chemistry is also closely related to other disciplines such as materials sciences, physical chemistry, thermodynamics, earth sciences,
mineralogy, crystallography, spectroscopy etc.
A chemical formula is a format used to express the structure of atoms. The formula tells which elements and how many of each
element are present in a compound. Formulas are written using the elemental symbol of each atom and a subscript to denote the
number of elements. This notation can be accredited to Swedish chemist Jons Jakob Berzeliu. The most common elements present
in organic compounds are carbon, hydrogen, oxygen, and nitrogen. With carbon and hydrogen present, other elements, such as
phosphorous, sulfur, silicon, and the halogens, may exist in organic compounds. Compounds that do not pertain to this rule are
called inorganic compounds.

Molecular Geometry and Structural Formula

Understanding how atoms in a molecules are arranged and how they are bonded together is very important in giving the molecule
its identity. Isomers are compounds in which two molecules can have the same number of atoms, and thus the same molecular
formula, but can have completely different physical and chemical properties because of differences in structural formula.

Methylpropane and butane have the same molecular formula of C4H10, but are structurally different (methylpropane on the left,
butane on the right).

Polymers
A polymer is formed when small molecules of identical structure, monomers, combine into a large cluster. The monomers are
joined together by covalent bonds. When monomers repeat and bind, they form a polymer. While they can be comprised of natural
or synthetic molecules, polymers often include plastics and rubber. When a molecule has more than one of these polymers, square
parenthesis are used to show that all the elements within the polymer are multiplied by the subscript outside of the parenthesis. The
subscript (shown as n in the example below) denotes the number of monomers present in the macromolecule (or polymer).

Ethylene becomes the polymer polyethylene.

Molecular Formula
The molecular formula is based on the actual makeup of the compound. Although the molecular formula can sometimes be the
same as the empirical formula, molecular compounds tend to be more helpful. However, they do not describe how the atoms are
put together. Molecular compounds are also misleading when dealing with isomers, which have the same number and types of
atoms (see above in molecular geometry and structural formula).

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Ex. Molecular Formula for Ethanol: C2H6O.

Empirical Formula
An empirical formula shows the most basic form of a compound. Empirical formulas show the number of atoms of each element in
a compound in the most simplified state using whole numbers. Empirical formulas tend to tell us very little about a compound
because one cannot determine the structure, shape, or properties of the compound without knowing the molecular formula.
Usefulness of the empirical formula is decreased because many chemical compounds can have the same empirical formula.

Ex. Find the empirical formula for C8H16O2.

Answer: C4H8O (divide all subscripts by 2 to get the smallest, whole number ratio).

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

Ex. Structural Formula for Ethanol:

Condensed Structural Formula

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

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

Ex. Line-Angle Formula for Ethanol:

Formulas of Inorganic Compounds

Inorganic compounds are typically not of biological origin. Inorganic compounds are made up of atoms connected using ionic
bonds. These inorganic compounds can be binary compounds, binary acids, or polyatomic ions.

Binary compounds
Binary compounds are formed between two elements, either a metal paired with a nonmetal or two nonmetals paired together.
When a metal is paired with a nonmetal, they form ionic compounds in which one is a negatively charged ion and the other is
positvely charged. The net charge of the compound must then become neutral. Transition metals have different charges; therefore,
it is important to specify what type of ion it is during the naming of the compound. When two nonmetals are paired together, the
compound is a molecular compound. When writing out the formula, the element with a positive oxidation state is placed first.
Ex. Ionic Compound: BaBr2(Barium Bromide)
Ex. Molecular Compound: N2O4 (Dinitrogen Tetroxide)

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Binary acids
Binary acids are binary compounds in which hydrogen bonds with a nonmetal forming an acid. However, there are exceptions such
as NH3, which is a base. This is because it shows no tendency to produce a H+. Because hydrogen is positively charged, it is placed
first when writing out these binary acids.
Ex. HBr (Hydrobromic Acid)

Polyatomic ions
Polyatomic ions is formed when two or more atoms are connected with covalent bonds. Cations are ions that have are postively
charged, while anions are negatively charged ions. The most common polyatomic ions that exists are those of anions. The two main
polyatomic cations are Ammonium and Mercury (I). Many polyatomic ions are typically paired with metals using ionic bonds to
form chemical compounds.
Ex. MnO4- (Polyatomic ion); NaMnO4 (Chemical Compound)

Oxoacids
Many acids have three different elements to form ternary compounds. When one of those three elements is oxygen, the acid is
known as a oxoacid. In other words, oxacids are compounds that contain hydrogen, oxgygen, and one other element.
Ex. HNO3 (Nitric Acid)

Complex Compounds
Certain compounds can appear in multiple forms yet mean the same thing. A common example is hydrates: water molecules bond
to another compound or element. When this happens, a dot is shown between H2O and the other part of the compound. Because the
H2O molecules are embedded within the compound, the compound is not necessarily "wet". When hydrates are heated, the water in
the compound evaporates and the compound becomes anhydrous. These compounds can be used to attract water such as CoCl2.
When CoCl2 is dry, CoCl2 is a blue color wherease the hexahydrate (written below) is pink in color.

·
Ex. CoCl2 6 H2O

Formulas of Organic Compounds

Organic compounds contain a combination carbon and hydrogen or carbon and hydrogen with nitrogen and a few other elements,
such as phosphorous, sulfur, silicon, and the halogens. Most organic compounds are seen in biological origin, as they are found in
nature.

Hydrocarbons
Hydrocarbons are compounds that consist of only carbon and hydrogen atoms. Hydrocarbons that are bonded together with only
single bonds are alkanes. The simplest example is methane (shown below). When hydrocarbons have one or more double bonds,
they are called alkenes. The simplest alkene is Ethene (C2H4) which contains a double bond between the two carbon atoms.

Ex. Methane on left, Ethene on right

Functional Groups
Functional groups are atoms connected to carbon chains or rings of organic molecules. Compounds that are within a functional
group tend to have similar properties and characteristics. Two common functional groups are hydroxyl groups and carboxyl groups.
Hydroxyl groups end in -OH and are alcohols. Carboxyl groups end in -COOH, making compounds containing -COOH carboxylic
acids. Functional groups also help with nomenclature by using prefixes to help name the compounds that have similar chemical
properties.

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Ex. Hydroxyl Group on top; Carboxyl Group on bottom

References
1. Miessler, Gary L. Inorganic Chemistry. 2nd. Upper Saddle River: Prentince Hall, 1999.
2. Munowitz, Michael. Principles of Chemistry. Norton & Company: New York, 2000.
3. Pettrucci, Ralph H. General Chemistry: Principles and Modern Applications. 9th. Upper Saddle River: Pearson Prentice Hall,
2007.

Problems
1. Which of the following formulas are organic?
a. HClO
b. C5H10
c. CO2
2. What is the name of the following formula?

3. Classify the following formulas into their appropriate functional group

a. Acetic acid
b. Butanol
c. Oxalic acid
4. What are the empirical formulas for the following compounds?
a. C12H10O6
b. CH3CH2CH2CH2CH2CH2CH3
c. H3O
5. What is the name of the following figure and what is the molecular formula of the following figure?

Answer Key:
1. b and c. 2. Propane. 3. a. carboxyl group, b. hydroxyl group, c. carboxyl group. 4. a. C6H5O3, b. C7H16, c. H3O. 5. Methylbutane,
C5H12

Contributors and Attributions

Jean Kim (UCD), Kristina Bonnett (UCD)

Further Reading

MasterOrganicChemistry
The Many Ways of Drawing Butane
Hidden Hydrogens, Hidden Lone Pairs, Hidden Counterions

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The Principle of Least Effort
Condensed Formulas: Deciphering the Brackets
Common Mistakes: Pentavalent Carbon
Khan Academy
Organic Structures
Representing Organic Molecules
Leah4Sci
Drawing Skeletal Structures of Bond-Line Notations of Organic Molecules
Web Pages
Condensed formulas
Molecular formula, structural formula, 3-dimensions
Videos
Line structures
Condensed Formulas
1.9: Representation of Molecular Structure is shared under a CC BY-NC-SA 4.0 license and was authored, remixed, and/or curated by LibreTexts.
Formulas of Inorganic and Organic Compounds is licensed CC BY-NC-SA 4.0.

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1.10: Pi Conjugation
A conjugated system is a system of connected p-orbitals with delocalized electrons in compounds with alternating single and multiple bonds, which in general may lower the overall
energy of the molecule and increase stability. Lone pairs, radicals or carbenium ions may be part of the system. The compound may be cyclic, acyclic, linear or mixed.
Conjugation is the overlap of one p-orbital with another across an intervening sigma bond (in larger atoms d-orbitals can be involved).[1]
A conjugated system has a region of overlapping p-orbitals, bridging the interjacent single bonds. They allow a delocalization of pi electrons across all the adjacent aligned p-orbitals.[2]
The pi electrons do not belong to a single bond or atom, but rather to a group of atoms.
The largest conjugated systems are found in graphene, graphite, conductive polymers, and carbon nanotubes.

Mechanism
Conjugation is possible by means of alternating single and double bonds. As long as each contiguous atom in a chain has an available p-orbital, the system can be considered
conjugated. For example, furan (see picture) is a five-membered ring with two alternating double bonds and an oxygen in position 1. Oxygen has two lone pairs, one of which occupies a
p-orbital on that position, thereby maintaining the conjugation of that five-membered ring. The presence of a nitrogen in the ring or groups α to the ring like a carbonyl group (C=O), an
imine group (C=N), a vinyl group (C=C), or an anion will also suffice as a source of pi orbitals to maintain conjugation.
There are also other ways of conjugation. Homoconjugation[3] is an overlap of two π-systems separated by a non-conjugating group, such as CH2. For example, the molecule
CH2=CH–CH2–CH=CH2 (1,4-pentadiene) is homoconjugated because the two C=C double bonds (which are π-systems because each double bond contains one π bond) are separated
by one CH2 group.[4]

Conjugated systems in pigments

Conjugated systems have unique properties that give rise to strong colors. Many pigments make use of conjugated electron systems, such as the long conjugated hydrocarbon chain in
beta-carotene, resulting in a strong orange color. When an electron in the system absorbs a photon of light of the right wavelength, it can be promoted to a higher energy level. (See
particle in a box). Most of these electronic transitions are from one conjugated π-system molecular orbital (MO) with an even kind of symmetry to another conjugated π-system MO
with an odd kind of symmetry (π to π*), but electrons from other states can also be promoted to a π-system MO (n to π*) as often happens in charge-transfer complexes. Often a HOMO
to LUMO transition is made by an electron if it is allowed by the selection rules for electromagnetic transitions. Conjugated systems of fewer than eight conjugated double bonds absorb
only in the ultraviolet region and are colorless to the human eye. With every double bond added, the system absorbs photons of longer wavelength (and lower energy), and the
compound ranges from yellow to red in color. Compounds that are blue or green typically do not rely on conjugated double bonds alone.
This absorption of light in the ultraviolet to visible spectrum can be quantified using ultraviolet–visible spectroscopy, and forms the basis for the entire field of photochemistry.
Conjugated systems that are widely used for synthetic pigments and dyes are diazo and azo compounds and phthalocyanine compounds.

Phthalocyanine compounds
Conjugated systems not only have low energy excitations in the visible spectral region but they also accept or donate electrons easily. Phthalocyanines, which, like Phthalo Blue and
Phthalo Green, often contain a transition metal ion, exchange an electron with the complexed transition metal ion that easily changes its oxidation state. Pigments and dyes like these are
charge-transfer complexes.

Copper phthalocyanine

Porphyrins and similar compounds

Porphyrins have conjugated molecular ring systems (macrocycles) that appear in many enzymes of biological systems. As a ligand, porphyrin forms numerous complexes with metallic
ions like iron in hemoglobin that colors blood red. Hemoglobin transports oxygen to the cells of our bodies. Porphyrin–metal complexes often have strong colors. A similar molecular
structural ring unit called chlorin is similarly complexed with magnesium instead of iron when forming part of the most common forms of chlorophyll molecules, giving them a green
color. Another similar macrocycle unit is corrin, which complexes with cobalt when forming part of cobalamin molecules, constituting Vitamin B12, which is intensely red. The corrin
unit has six conjugated double bonds but is not conjugated all the way around its macrocycle ring.

The chlorin section of the chlorophyll a molecule. The green box shows a group
Heme group of hemoglobin Cobalamin structure includes a corrin macrocycle.
that varies between chlorophyll types.

Chromophores
Conjugated systems form the basis of chromophores, which are light-absorbing parts of a molecule that can cause a compound to be colored. Such chromophores are often present in
various organic compounds and sometimes present in polymers that are colored or glow in the dark. Chromophores often consist of a series of conjugated bonds and/or ring systems,
commonly aromatic, which can include C–C, C=C, C=O, or N=N bonds.

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Chemical structure of beta-carotene. The eleven conjugated double bonds that form the chromophore of
the molecule are highlighted in red.
Conjugated chromophores are found in many organic compounds including azo dyes (also artificial food additives), compounds in fruits and vegetables (lycopene and anthocyanidins),
photoreceptors of the eye, and some pharmaceutical compounds such as the following:

This polyene antimycotic called Amphotericin B has a conjugated system with seven double
bonds acting as a chromophore that absorbs strongly in the ultraviolet–visible spectrum, giving it
a yellow color.

Further Reading

Carey 4th Edition Online

Conjugation

Web Pages
Conjugation
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1.11: Aromaticity
Aromaticity is a property of conjugated cycloalkenes in which the stabilization of the molecule is enhanced due to the ability of the
electrons in the π orbitals to delocalize. This act as a framework to create a planar molecule.

Introduction
Why do we care if a compound is aromatic or not? Because we encounter aromatics every single day of our lives. Without aromatic
compounds, we would not only be lacking many material necessities, our bodies would also not be able to function. Aromatic
compounds are essential in industry; about 35 million tons of aromatic compounds are produced in the world every year to produce
important chemicals and polymers, such as polyester and nylon. Aromatic compounds are also vital to the biochemistry of all living
things. Three of the twenty amino acids used to form proteins ("the building blocks of life") are aromatic compounds and all five of
the nucleotides that make up DNA and RNA sequences are all aromatic compounds. Needless to say, aromatic compounds are vital
to us in many aspects.
The three general requirements for a compound to be aromatic are:
1. The compound must be cyclic
2. Each element within the ring must have a p-orbital that is perpendicular to the ring, hence the molecule is planar.
3. The compound must follow Hückel's Rule (the ring has to contain 4n+2 p-orbital electrons).
Among the many distinctive features of benzene, its aromaticity is the major contributor to why it is so unreactive. This section will
try to clarify the theory of aromaticity and why aromaticity gives unique qualities that make these conjugated alkenes inert to
compounds such as Br2 and even hydrochloric acid. It will also go into detail about the unusually large resonance energy due to the
six conjugated carbons of benzene.

The delocalization of the p-orbital carbons on the sp2 hybridized carbons is what gives the aromatic qualities of benzene.

Basic Structue of Benzene

Because of the aromaticity of benzene, the resulting molecule is planar in shape with
each C-C bond being 1.39 Å in length and each bond angle being 120°. You might ask
yourselves how it's possible to have all of the bonds to be the same length if the ring is
conjugated with both single (1.47 Å) and double (1.34 Å), but it is important to note that
there are no distinct single or double bonds within the benzene. Rather, the
delocalization of the ring makes each count as one and a half bonds between the carbons
which makes sense because experimentally we find that the actual bond length is
somewhere in between a single and double bond. Finally, there are a total of six p-
orbital electrons that form the stabilizing electron clouds above and below the aromatic
ring.

Evidence of Aromaticity: Heats of Hydrogenation

One of the ways to test the relative amounts of resonance energy in a molecule is to compare the heats of hydrogenation between
similar compounds. For instance, if we compare cyclohexene, 1,3-cyclohexadiene, and benzene, we would expect that their heats
of hydrogenation will increase since the number of double bonds increases respectively. However, experimental evidence suggests
that the actual heat of hydrogenation for benzene is actually 49.3 kcal/mole, making it even more stable than the 1,3-
cyclohexadiene even though it has two double bonds, compared to benzene's three double bonds. This characteristic can be
attributed to the aromaticity of benzene which delocalizes the electrons of the six pi orbitals.

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References
1. P. Schleyer, "Aromaticity (Editorial)", Chemical Reviews, 2001.
2. P. Schleyer, "Introduction: Delocalization-? and ? (Editorial)", Chemical Reviews, 2005.
3. Vollhardt, K. Peter C., and Neil E. Schore. Organic Chemistry: Structure and Function. New York: W.H. Freeman and
Company, 2007.

Problems
1. What is the hybridization of each carbon and the overall shape of benzene?
2. What is the resonance energy of benzene?
3. Place the following compounds in order of heats of hydrogenation from smallest to greatest : Benzene, 1,3-Cyclohexadiene, and
Cyclohexene.

Answers
1. All six carbons are sp2 hybridized and the aromaticity of the benzene creates a planar molecule.
2. 29.6 kcal/mol
3. Cyclohexene < Benzene < 1,3-Cyclohexadiene.

Contributors
Ramie Hosein

Further Reading

MasterOrganicChemistry
What Does 4n+2 Mean?

Khan Academy
Aromatic Stability-I
Aromatic Stability-II
Carey 4th Ed Online
Aromaticity

Web Pages
Aromaticity
Aromaticity Tutorial

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 Aromaticity Theory
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Aromaticity is licensed CC BY-NC-SA 4.0.

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 CHAPTER OVERVIEW

Chapter 2. Functional Groups and Nomenclature

Purdue CHM 26505: Organic

Chemistry for Chemistry Majors (1st
Semester)
Fall 2014: Prof. Mark Lipton

Template:HideTOC
2.1: Alkanes
2.1B: Cycloalkanes
2.2: Alkenes
2.3: Alkynes
2.4: Arenes
2.5: Functional Groups
2.5: Alcohols
2.6: Ethers, Epoxides and Sulfides
2.7: Amines
2.8: Aldehydes and Ketones
2.9: Carboxylic Acids
2.10: Esters, Amides, Acid Halides, Anhydrides and Nitriles
Appendix - IUPAC Nomenclature Rules

Chapter 2. Functional Groups and Nomenclature is shared under a CC BY-NC-SA 4.0 license and was authored, remixed, and/or curated by LibreTexts.

1
2.1: Alkanes
Alkanes are hydrocarbons that can be described by the general formula CnH2n+2. They consist only of carbon and hydrogen and
contain only single bonds. Alkanes are also known as "saturated hydrocarbons."
The following table contains the systematic names for the first twenty straight chain alkanes. It will be important to familiarize
yourself with these names because they will be the basis for naming many other organic molecules throughout your course of study.

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

Using Common Names with Branched Alkanes

Certain branched alkanes have common names that are still widely used today. These common names make use of prefixes, such as
iso-, sec-, tert-, and neo-. The prefix iso-, which stands for isomer, is commonly given to 2-methyl alkanes. In other words, if there
is methyl group located on the second carbon of a carbon chain, we can use the prefix iso-. The prefix will be placed in front of the
alkane name that indicates the total number of carbons.
Examples:
isopentane which is the same as 2-methylbutane
isobutane which is the same as 2-methylpropane
To assign the prefixes sec-, which stands for secondary, and tert-, for tertiary, it is important that we first learn how to classify
carbon molecules. If a carbon is attached to only one other carbon, it is called a primary carbon. If a carbon is attached to two
other carbons, it is called a seconday carbon. A tertiary carbon is attached to three other carbons and last, a quaternary carbon is
attached to four other carbons.

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Examples:
4-sec-butylheptane (30g)
4-tert-butyl-5-isopropylhexane (30d); if using this example, may want to move sec/tert after iso disc
The prefix neo-
Examples:
neopentane
neoheptane

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

The same approach can be used with any of the alkanes in the table above and with common names.

Three Basic Principles of Naming

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

Example

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

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

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 next example.

Example

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

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

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

Example

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

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

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

Once you have determined the correct numbering of the carbons, it is often useful to make a list, including the functional groups, substitutes, and
the name of the parent chain.
Parent chain: heptane 2-Chloro 3-Methyl 6-Bromo
6-bromo-2-chloro-3-methylheptane

Problems

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2.1: Alkanes is shared under a CC BY-NC-SA 4.0 license and was authored, remixed, and/or curated by LibreTexts.

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2.1B: Cycloalkanes
Cycloalkanes are cyclic hydrocarbons, meaning that the carbons of the molecule are arranged in the form of a ring. Cycloalkanes
are also saturated, meaning that all of the carbons atoms that make up the ring are single bonded to other atoms (no double or triple
bonds). There are also polycyclic alkanes, which are molecules that contain two or more cycloalkanes that are joined, forming
multiple rings.

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

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

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

flat molecules. All of the cycloalkanes, from cyclopentane upwards, exist as "puckered rings". Cyclohexane, for example, has a
ring structure that looks like this:

Figure 2: This is known as the "chair" form of cyclohexane from its shape, which vaguely resembles a chair. Note: The
cyclohexane molecule is constantly changing, with the atom on the left, which is currently pointing down, flipping up, and the atom
on the right flipping down. During this process, another (slightly less stable) form of cyclohexane is formed known as the "boat"
form. In this arrangement, both of these atoms are either pointing up or down at the same time
In addition to being saturated cyclic hydrocarbons, cycloalkanes may have multiple substituents or functional groups that further
determine their unique chemical properties. The most common and useful cycloalkanes in organic chemistry are cyclopentane and
cyclohexane, although other cycloalkanes varying in the number of carbons can be synthesized. Understanding cycloalkanes and
their properties are crucial in that many of the biological processes that occur in most living things have cycloalkane-like structures.

Glucose (6 carbon sugar) Ribose (5 carbon sugar) Cholesterol (polycyclic)

Although polycyclic compounds are important, they are highly complex and typically have common names accepted by IUPAC.
However, the common names do not generally follow the basic IUPAC nomenclature rules. The general formula of the
cycloalkanes is C H where n is the number of carbons. The naming of cycloalkanes follows a simple set of rules that are built
n 2n

upon the same basic steps in naming alkanes. Cyclic hydrocarbons have the prefix "cyclo-".

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Contents
For simplicity, cycloalkane molecules can be drawn in the form of skeletal structures in which each intersection between two lines
is assumed to have a carbon atom with its corresponding number of hydrogens.

same as same as

Cycloalkane Molecular Formula Basic Structure

Cyclopropane C3H6

Cyclobutane C4H8

Cyclopentane C5H10

Cyclohexane C6H12

Cycloheptane C7H14

Cyclooctane C8H16

Cyclononane C9H18

Cyclodecane C10H20

IUPAC Rules for Nomenclature

1. Determine the cycloalkane to use as the parent chain. The parent chain is the one with the highest number of carbon atoms. If
there are two cycloalkanes, use the cycloalkane with the higher number of carbons as the parent chain.
2. If there is an alkyl straight chain that has a greater number of carbons than the cycloalkane, then the alkyl chain must be used as
the primary parent chain. Cycloalkane acting as a substituent to an alkyl chain has an ending "-yl" and, therefore, must be
named as a cycloalkyl.

Cycloalkane Cycloalkyl
cyclopropane cyclopropyl
cyclobutane cyclobutyl
cyclopentane cyclopentyl
cyclohexane cyclohexyl

cycloheptane cycloheptyl
cyclooctane cyclooctyl
cyclononane cyclononanyl
cyclodecane cyclodecanyl

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 Example

The longest straight chain contains 10 carbons, compared with cyclopropane, which only contains 3 carbons. Because cyclopropane is a
substituent, it would be named a cyclopropyl-substituted alkane.

3) Determine any functional groups or other alkyl groups.

4) Number the carbons of the cycloalkane so that the carbons with functional groups or alkyl groups have the lowest possible
number. A carbon with multiple substituents should have a lower number than a carbon with only one substituent or functional
group. One way to make sure that the lowest number possible is assigned is to number the carbons so that when the numbers
corresponding to the substituents are added, their sum is the lowest possible.

(1+3=4) NOT (1+5=6)

5) When naming the cycloalkane, the substituents and functional groups must be placed in alphabetical order.

(ex: 2-bromo-1-chloro-3-methylcyclopentane)
6) Indicate the carbon number with the functional group with the highest priority according to alphabetical order. A dash"-" must
be placed between the numbers and the name of the substituent. After the carbon number and the dash, the name of the substituent
can follow. When there is only one substituent on the parent chain, indicating the number of the carbon atoms with the substituent
is not necessary.

(ex: 1-chlorocyclohexane or cholorocyclohexane is acceptable)

7) If there is more than one of the same functional group on one carbon, write the number of the carbon two, three, or four times,
depending on how many of the same functional group is present on that carbon. The numbers must be separated by commas, and
the name of the functional group that follows must be separated by a dash. When there are two of the same functional group, the
name must have the prefix "di". When there are three of the same functional group, the name must have the prefix "tri". When there
are four of the same functional group, the name must have the prefix "tetra". However, these prefixes cannot be used when
determining the alphabetical priorities.
There must always be commas between the numbers and the dashes that are between the numbers and the names.

Example 2

(2-bromo-1,1-dimethylcyclohexane)

Notice that "f" of fluoro alphabetically precedes the "m" of methyl. Although "di" alphabetically precedes "f", it is not used in
determining the alphabetical order.

Example 3

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 (2-fluoro-1,1,-dimethylcyclohexane NOT 1,1-dimethyl-2-fluorocyclohexane)

8) If the substituents of the cycloalkane are related by the cis or trans configuration, then indicate the configuration by placing "cis-
" or "trans-" in front of the name of the structure.

Blue=Carbon Yellow=Hydrogen Green=Chlorine

Notice that chlorine and the methyl group are both pointed in the same direction on the axis of the molecule; therefore, they are cis.

cis-1-chloro-2-methylcyclopentane
9) After all the functional groups and substituents have been mentioned with their corresponding numbers, the name of the
cycloalkane can follow.

Summary
1. Determine the parent chain: the parent chain contains the most carbon atoms.
2. Number the substituents of the chain so that the sum of the numbers is the lowest possible.
3. Name the substituents and place them in alphabetical order.
4. If stereochemistry of the compound is shown, indicate the orientation as part of the nomenclature.
5. Cyclic hydrocarbons have the prefix "cyclo-" and have an "-alkane" ending unless there is an alcohol substituent present. When
an alcohol substituent is present, the molecule has an "-ol" ending.

Glossary
alkyl: A structure that is formed when a hydrogen atom is removed from an alkane.
cyclic: Chemical compounds arranged in the form of a ring or a closed chain form.
cycloalkanes: Cyclic saturated hydrocarbons with a general formula of CnH(2n). Cycloalkanes are alkanes with carbon atoms
attached in the form of a closed ring.
functional groups: An atom or groups of atoms that substitute for a hydrogen atom in an organic compound, giving the
compound unique chemical properties and determining its reactivity.
hydrocarbon: A chemical compound containing only carbon and hydrogen atoms.
saturated: All of the atoms that make up a compound are single bonded to the other atoms, with no double or triple bonds.
skeletal structure: A simplified structure in which each intersection between two lines is assumed to have a carbon atom with
its corresponding number of hydrogens.

Problems
Name the following structures. (Note: The structures are complex for practice purposes and may not be found in nature.)

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

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 7)
Draw the following structures.
8) 1,1-dibromo-5-fluoro-3-butyl-7-methylcyclooctane 9) trans-1-bromo-2-chlorocyclopentane
10) 1,1-dibromo-2,3-dichloro-4-propylcyclobutane 11) 2-methyl-1-ethyl-1,3-dipropylcyclopentane 12) cycloheptane-1,3,5-triol
Name the following structures.
Blue=Carbon Yellow=Hydrogen Red=Oxygen Green=Chlorine

13) 14) 15) 16) 17)

18) 19)

Answers to Practice Problems

1) cyclodecane 2) chlorocyclopentane or 1-chlorocyclopentane 3) trans-1-chloro-2-methylcycloheptane
4) 6-methyl-3-cyclopropyldecane 5) cyclopentylcyclodecane or 1-cyclopentylcyclodecane 6) 1,3-dibromo-1-chloro-2-
fluorocycloheptane
7) 1-cyclobutyl-4-isopropylcyclohexane

8) 9) 10) 11) 12)

13) cyclohexane 14) cyclohexanol 15) chlorocyclohexane 16) cyclopentylcyclohexane 17) 1-chloro-3-methylcyclobutane
18) 2,3-dimethylcyclohexanol 19) cis-1-propyl-2-methylcyclopentane

Outside links
More Practice Problems on Nomenclature of Cycloalkanes
Vollhardt, Schore. Organic Chemistry. 5th ed.
Wikipedia: Cycloalkanes
http://www.cem.msu.edu/~reusch/VirtualText/nomen1.htm
http://www.chemguide.co.uk/organicprops/alkanes/background.html
http://www.cem.msu.edu/~reusch/VirtualText/nomen1.htm
http://science.csustan.edu/nhuy/chem3010/handouts/HandoutIVNamecyal.htm
http://en.wikibooks.org/wiki/Organic_Chemistry/Alkanes_and_cycloalkanes/Cycloalkanes

References
1. ACD/ChemSketch Freeware, version 11.0, Advanced Chemistry Development, Inc., Toronto, ON, Canada, www.acdlabs.com,
2008.
2. Bruice, Paula Yurkanis. Oragnic Chemistry. 5th. CA. Prentice Hall, 2006.

2.1B.5 https://chem.libretexts.org/@go/page/16999
 3. Fryhle, C.B. and G. Solomons. Organic Chemistry. 9th ed. Danvers, MA: Wiley, 2008.
4. McMurry, John. Organic Chemistry. 7th ed. Belmont, California: Thomson Higher Education, 2008.
5. Sadava, Heller, Orians, Purves, Hillis. Life The Science of Biology. 8th ed. Sunderland, MA: W.H. Freeman, 2008.
6. Vollhardt, K. Peter C., and Neil E. Schore. Organic Chemistry. 5th ed. New York: W.H. Freeman, 2007.

Contributors
Pwint Zin
Jim Clark (ChemGuide)

2.1B: Cycloalkanes is shared under a CC BY-NC-SA 4.0 license and was authored, remixed, and/or curated by LibreTexts.

2.1B.6 https://chem.libretexts.org/@go/page/16999
2.2: Alkenes
Alkenes contain carbon-carbon double bonds and are unsaturated hydrocarbons with the molecular formula is CnH2n. This is also
the same molecular formula as cycloalkanes. Alkenes are named by dropping the -ane ending of the parent and adding -ene.

Introduction
The parent structure is the longest chain containing both carbon atoms of the double bond. The two carbon atoms of a double bond
and the four atoms attached to them lie in a plane, with bond angles of approximately 120° A double bond consists of one sigma
bond formed by overlap of sp2 hybrid orbitals and one pi bond formed by overlap of parallel 2 p orbitals

The Basic Rules

For straight chain alkenes, it is the same basic rules as nomenclature of alkanes except change the suffix to "-ene."
i. Find the Longest Carbon Chain that Contains the Carbon Carbon double bond. If you have two ties for longest Carbon
chain, and both chains contain a Carbon Carbon double bond, then identify the most substituted chain.
ii. Give the lowest possible number to the Carbon Carbon double bond.
1. Do not need to number cycloalkenes because it is understood that the double bond is in the one position.
2. Alkenes that have the same molecular formula but the location of the doble bonds are different means they are
constitutional isomers.
3. Functional Groups with higher priority:
iii. Add substituents and their position to the alkene as prefixes. Of course remember to give the lowest numbers possible.
And remember to name them in alphabetical order when writting them.
iv. Next is identifying stereoisomers. when there are only two non hydrogen attachments to the alkene then use cis and trans
to name the molecule.

In this diagram this is a cis conformation. It has both the substituents going upward. This molecule would be called (cis) 5-chloro-
3-heptene.)
Trans would look like this
v. On the other hand if there are 3 or 4 non-hydrogen different atoms attached to the alkene then use the E, Z system.
E (entgegen) means the higher priority groups are opposite one another relative to the double bond.
Z (zusammen) means the higher priority groups are on the same side relative to the double bond.
(You could think of Z as Zame Zide to help memorize it.)

In this example it is E-4-chloro-3-heptene. It is E because the Chlorine and the CH2CH3 are the two higher priorities and they are
on opposite sides.
vi. A hydroxyl group gets precedence over th double bond. Therefore alkenes containing alchol groups are called alkenols.
And the prefix becomes --enol. And this means that now the alcohol gets lowest priority over the alkene.

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 vii. Lastly remember that alkene substituents are called alkenyl. Suffix --enyl.
Here is a chart containing the systemic name for the first twenty straight chain alkenes.

Name Molecular formula

Ethene C2H4

Propene C3H6

Butene C4H8

Pentene C5H10

Hexene C6H12

Heptene C7H14

Octene C8H16

Nonene C9H18

Decene C10H20

Undecene C11H22

Dodecene C12H24

Tridecene C13H26

Tetradecene C14H28

Pentadecene C15H30

Hexadecene C16H32

Heptadecene C17H34

Octadecene C18H36

Nonadecene C19H38

Eicosene C20H40

Did you notice how there is no methene? Because it is impossible for a Carbon to have a double bond with nothing.

Geometric Isomers
Double bonds can exist as geometric isomers and these isomers are designated by using either the cis / trans designation or the
modern E / Z designation.

cis Isomers
.The two largest groups are on the same side of the double bond.

trans Isomers
...The two largest groups are on opposite sides of the double bond.

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E/Z nomenclature
E = entgegan ("trans") Z = zusamen ("cis")
Priority of groups is based on the atomic mass of attached atoms (not the size of the group). An atom attached by a multiple bond is
counted once for each bond.
fluorine atom > isopropyl group > n-hexyl group
deuterium atom > hydrogen atom
-CH2-CH=CH2 > -CH2CH2CH3

Example 1

Try to name the following compounds using both conventions...

Common names
Remove the -ane suffix and add -ylene. There are a couple of unique ones like ethenyl's common name is vinyl and 2-propenyl's
common name is allyl. That you should know are...
vinyl substituent H2C=CH-
allyl substituent H2C=CH-CH2-
allene molecule H2C=C=CH2
isoprene

Endocyclic Alkenes
Endocyclic double bonds have both carbons in the ring and exocyclic double bonds have only one carbon as part of the ring.

Cyclopentene is an example of an endocyclic double bond.

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Methylenecylopentane is an example of an exocyclic double bond.

Name the following compounds...

1-methylcyclobutene. The methyl group places the double bond. It is correct to also name this compound as 1-methylcyclobut-1-
ene.

1-ethenylcyclohexene, the methyl group places the double bond. It is correct to also name this compound as 1-ethenylcyclohex-1-
ene. A common name would be 1-vinylcyclohexene.
Try to draw structures for the following compounds...

2-vinyl-1,3-cyclohexadiene

Outside links
http://www.vanderbilt.edu/AnS/Chemis...0a/alkenes.pdf

References
1. Vollhardt, Peter, and Neil E. Schore. Organic Chemistry: Structure and Function. 5th Edition. New York: W. H. Freeman &
Company, 2007.

Problems
Try to name the following compounds...

1-pentene or pent-1-ene

2-ethyl-1-hexene or 2-ethylhex-1-ene
Try to draw structures for the following compounds...
2-pentene
CH3–CH=CH–CH2–CH3
3-heptene
CH3–CH2–CH=CH–CH2–CH2–CH3
b. Give the double bond the lowest possible numbers regardless of substituent placement.
• Try to name the following compound...

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 J
• Try to draw a structure for the following compound...
4-methyl-2-pentene J
Name the following structures:

v. Draw (Z)-5-Chloro-3-ethly-4-hexen-2-ol.

Answers
I. trans-8-ethyl-3-undecene
II. E-5-bromo-4-chloro-7,7-dimethyl-4-undecene
III. Z-1,2-difluoro-cyclohexene
IV. 4-ethenylcyclohexanol.

V.

Contributors
S. Devarajan (UCD)
Richard Banks (Boise State University)

2.2: Alkenes is shared under a CC BY-NC-SA 4.0 license and was authored, remixed, and/or curated by LibreTexts.

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2.3: Alkynes
Alkynes are organic molecules made of the functional group carbon-carbon triple bonds and are written in the empirical formula of
C H
n . They are unsaturated hydrocarbons. Like alkenes have the suffix –ene, alkynes use the ending –yne; this suffix is used
2n−2

when there is only one alkyne in the molecule.

Introduction

Here are the molecular formulas and names of the first ten carbon straight chain alkynes.

Name Molecular Formula

Ethyne C2H2

Propyne C3H4

1-Butyne C4H6

1-Pentyne C5H8

1-Hexyne C6H10

1-Heptyne C7H12

1-Octyne C8H14

1-Nonyne C9H16

1-Decyne C10H18

The more commonly used name for ethyne is acetylene, which used industrially.

Naming Alkynes
Like previously mentioned, the IUPAC rules are used for the naming of alkynes.

Rule 1
Find the longest carbon chain that includes both carbons of the triple bond.

Rule 2
Number the longest chain starting at the end closest to the triple bond. A 1-alkyne is referred to as a terminal alkyne and alkynes at
any other position are called internal alkynes.
For example:

4-chloro-6-diiodo-7-methyl-2-nonyne

Rule 3
After numbering the longest chain with the lowest number assigned to the alkyne, label each of the substituents at its corresponding
carbon. While writing out the name of the molecule, arrange the substituents in alphabetical order. If there are more than one of the
same substituent use the prefixes di, tri, and tetra for two, three, and four substituents respectively. These prefixes are not taken into
account in the alphabetical order.
For example:

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1-triiodo-4-dimethyl-2-nonyne
If there is an alcohol present in the molecule, number the longest chain starting at the end closest to it, and follow the same rules.
However, the suffix would be –ynol, because the alcohol group takes priority over the triple bond.

5- methyl-7-octyn-3-ol
When there are two triple bonds in the molecule, find the longest carbon chain including both the triple bonds. Number the longest
chain starting at the end closest to the triple bond that appears first. The suffix that would be used to name this molecule would be –
diyne.
For example:

4-methyl-1,5-octadiyne

Rule 4
Substituents containing a triple bond are called alkynyl.
For example:

1-chloro-1-ethynyl-4-bromocyclohexane
Here is a table with a few of the alkynyl substituents:

Name Molecule

Ethynyl -C?CH

2- Propynyl -CH2C?CH

2-Butynyl -CH3C?CH2CH3

Rule 5
A molecule that contains both double and triple bonds is called an alkenyne. The chain can be numbered starting with the end
closest to the functional group that appears first. For example:

6-ethyl-3-methyl-1,4-nonenyne

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Outside links
http://en.wikipedia.org/wiki/Alkyne
http://www.cem.msu.edu/~reusch/VirtualText/nomen1.htm

Reference
1. Vollhardt, Peter, and Neil E. Schore. Organic Chemistry: Structure and Function. 5th Edition. New York: W. H. Freeman &
Company, 2007.

Problems
Name or draw out the following molecules:
1. 4,4-dimethyl-2-pentyne
2. 4-Penten-1-yne
3. 1-ethyl-3-dimethylnonyne
4.

Contributors
A. Sheth and S. Sujit (UCD)

2.3: Alkynes is shared under a CC BY-NC-SA 4.0 license and was authored, remixed, and/or curated by LibreTexts.

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2.4: Arenes
Benzene, C6H6, as shown on the left, is an organic aromatic compound with many interesting properties. Unlike
aliphatic (straight chain carbons) or other cyclic organic compounds, the structure of benzene (3 conjugated π bonds)
allows benzene and its derived products to be useful in fields such as health, laboratorial, and other applications such
as rubber synthesis.

Introduction
Benzene derived products are well known to be pleasantly fragrant. For this reason, organic compounds containing benzene rings
were classified as being "aromatic" (sweet smelling) amongst scientists in the early 19th century when a relation was established
between benzene derived compounds and sweet/spicy fragrances. There is a misconception amongst the scientific community,
however, that all aromatics are sweet smelling and that all sweet smelling compounds would have a benzene ring in its structure.
This is false, since non-aromatic compounds, such as camphor, extracted from the camphor laurel tree, release a strong, minty
aroma, yet it lacks the benzene ring in its structure (See figure 1). On the other hand, benzene itself gives off a rather strong and
unpleasant smell that would otherwise invalidate the definition of an aromatic (sweet-smelling) compound. Despite this
inconsistency, however, the term aromatic continues to be used today in order to designate molecules with benzene-like rings in
their structures. For a modern, chemical definition of aromaticity, refer to sections Aromaticity and Hückel's Rule.

Figure 1. Top-view of camphor, along with its monoterpene unit. Notice how camphor lacks the benzene ring to be "aromatic".
Many aromatic compounds are however, sweet/pleasant smelling. Eugenol, for example, is extracted from essential oils of cloves
and it releases a spicy, clove-like aroma used in perfumes. In addition, it is also used in dentistry as an analgesic.

Figure 2. Eugenol, an aromatic compound extracted from clove essential oils. Used in perfumes and as an analgesic.
The benzene ring is labeled in red in the eugenol molecule.

Is it cyclohexane or is it benzene?
Due to the similarity between benzene and cyclohexane, the two is often confused with each other in beginning organic chemistry
students.

Figure 3. Structure comparison between cyclohexane and benzene

If you were to count the number of carbons and hydrogens in cyclohexane, you will notice that its molecular formula is C6H12.
Since the carbons in the cyclohexane ring is fully saturated with hydrogens (carbon is bound to 2 hydrogens and 2 adjacent
carbons), no double bonds are formed in the cyclic ring. In contrast, benzene is only saturated with one hydrogen per carbon,
leading to its molecular formula of C6H6. In order to stabilize this structure, 3 conjugated π (double) bonds are formed in the
benzene ring in order for carbon to have four adjacent bonds.

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In other words, cyclohexane is not the same as benzene! These two compounds have different molecular formulas and their
chemical and physical properties are not the same. The hydrogenation technique can be used by chemists to convert from benzene
to cyclohexane by saturating the benzene ring with missing hydrogens.
IMPORTANT NOTE: A special catalyst is required to hydrogenate benzene rings due to its unusual stability and configuration.
Normal catalytic hydrogenation techniques will not hydrogenate benzene and yield any meaningful products.

What about Resonance?

Benzene can be drawn a number of different ways. This is because benzene's conjugated pi electrons freely resonate within the
cyclic ring, thus resulting in its two resonance forms.
Figure 4. The figure to the left shows the two resonance forms of benzene. The delocalized electrons
are moved from one carbon to the next, thus providing stabilization energy. Ring structures stabilized
by the movement of delocalized electrons are sometimes referred to as arenes.

As the electrons in the benzene ring can resonate within the ring at a fairly high rate, a simplified notation is often used to designate
the two different resonance forms. This notation is shown above, with the initial three pi bonds (#1, #2) replaced with an inner ring
circle (#3). Alternatively, the circle within the benzene ring can also be dashed to show the same resonance forms (#4).

The Formation of the Phenyl Group and its Derivatives

The phenyl group can be formed by taking benzene, and removing a hydrogen from it. The resulting molecular formula for the
fragment is C6H5. NOTE: Although the molecular formula of the phenyl group is C6H5, the phenyl group would always have
something attached to where the hydrogen was removed. Thus, the formula is often written as Ph-R, where Ph refers to the Phenyl
group, and R refers to the R group attached to where the hydrogen was removed.

Figure 5. Figure demonstrating the removal of hydrogen to form the phenyl group.
Different R groups on the phenyl group allows different benzene derivatives to be formed. Phenol, Ph-OH, or C6H5OH, for
example, is formed when an alcohol (-OH) group displaces a hydrogen atom on the benzene ring. Benzene, for this very same
reason, can be formed from the phenyl group by reattaching the hydrogen back its place of removal. Thus benzene, similar to
phenol, can be abbreviated Ph-H, or C6H6.

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Figure 7. (Left): Epigallocatechin gallate (EGCG), an antioxidant found in green teas and its extracts, is famous for its potential
health benefits. The molecule is a type of catechin, which is composed of multiple phenol (labeled in red) units (polyphenols -
see polycyclic aromatics). Since catechins are usually found in plant extracts, they are often referred as plant polyphenolic
antioxidants.
As you can see above, these are only some of the many possibilities of the benzene derived products that have special uses in
human health and other industrial fields.

Nomenclature of Benzene Derived Compounds

Unlike aliphatic organics, nomenclature of benzene-derived compounds can be confusing because a single aromatic compound can
have multiple possible names (such as common and systematic names) be associated with its structure. In these sections, we will
analyze some of the ways these compounds can be named.

Simple Benzene Naming

Some common substituents, like NO2, Br, and Cl, can be named this way when it is attached to a phenyl group. Long chain carbons
attached can also be named this way. The general format for this kind of naming is:
(positions of substituents (if >1)- + # (di, tri, ...) + substituent)n + benzene.
For example, chlorine (Cl) attached to a phenyl group would be named chlorobenzene (chloro + benzene). Since there is only one
substituent on the benzene ring, we do not have to indicate its position on the benzene ring (as it can freely rotate around and you
would end up getting the same compound.)

Figure 8. Example of simple benzene naming with chlorine and NO2 as substituents.

Figure 9. More complicated simple benzene naming examples - Note that standard nomenclature priority rules are applied here,
causing the numbering of carbons to switch. See Nomenclature of Organic Compounds for a review on naming and priority rules.

Ortho-, Meta-, Para- (OMP) Nomenclature for Disubstituted Benzenes

Instead of using numbers to indicate substituents on a benzene ring, ortho- (o-), meta- (m-), or para (p-) can be used in place of
positional markers when there are two substituents on the benzene ring (disubstituted benzenes). They are defined as the following:
ortho- (o-): 1,2- (next to each other in a benzene ring)
meta- (m): 1,3- (separated by one carbon in a benzene ring)
para- (p): 1,4- (across from each other in a benzene ring)
Using the same example above in figure 9a (1,3-dichlorobenzene), we can use the ortho-, meta-, para- nomenclature to transform
the chemical name into m-dichlorobenzene, as shown in the figure below.

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 Figure 10. Transformation of 1,3-dichlorobenzene into m-dichlorobenzene.
Here are some other examples of ortho-, meta-, para- nomenclature used in context:

However, the substituents used in ortho-, meta-, para- nomenclature do not have to be the same. For example, we can use chlorine
and a nitro group as substituents in the benzene ring.

In conclusion, these can be pieced together into a summary diagram, as shown below:

Base Name Nomenclature

In addition to simple benzene naming and OMP nomenclature, benzene derived compounds are also sometimes used as bases. The
concept of a base is similar to the nomenclature of aliphatic and cyclic compounds, where the parent for the organic compound is
used as a base (a name for its chemical name.
For example, the following compounds have the base names hexane and cyclohexane, respectively.
See Nomenclature of Organic Compounds for a review on naming organic compounds.

Benzene, similar to these compounds shown above, also has base names from its derived compounds. Phenol (C6H5OH), as
introduced previously in this article, for example, serves as a base when other substituents are attached to it. This is best illustrated
in the diagram below.

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Figure 14. An example showing phenol as a base in its chemical name. Note how benzene no longer serves as a base when an OH
group is added to the benzene ring.
Alternatively, we can use the numbering system to indicate this compound. When the numbering system is used, the carbon where
the substituent is attached on the base will be given the first priority and named as carbon #1 (C1). The normal priority rules then
apply in the nomenclature process (give the rest of the substituents the lowest numbering as you could).

Figure 15. The naming process for 2-chlorophenol (o-chlorophenol). Note that 2-chlorophenol = o-chlorophenol.
Below is a list of commonly seen benzene-derived compounds. Some of these mono-substituted compounds (labeled in red and
green), such as phenol or toluene, can be used in place of benzene for the chemical's base name.

Figure 16. Common benzene derived compounds with various substituents.

Common vs. Systematic (IUPAC) Nomenclature

According to the indexing preferences of the Chemical Abstracts, phenol, benzaldehyde, and benzoic acid (labeled in red in
Figure 16) are some of the common names that are retained in the IUPAC (systematic) nomenclature. Other names such as toluene,
styrene, naphthalene, or phenanthrene can also be seen in the IUPAC system in the same way. While the use of other common
names are usually acceptable in IUPAC, their use are discouraged in the nomenclature of compounds.
Nomenclature for compounds which has such discouraged names will be named by the simple benzene naming system. An
example of this would include toluene derivatives like TNT. (Note that toluene by itself is retained by the IUPAC nomenclature,
but its derivatives, which contains additional substituents on the benzene ring, might be excluded from the convention). For this
reason, the common chemical name 2,4,6-trinitrotoluene, or TNT, as shown in figure 17, would not be advisable under the IUPAC
(systematic) nomenclature.
In order to correctly name TNT under the IUPAC system, the simple benzene naming system should be used:

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 Figure 18. Systematic (IUPAC) name of 2,4,6-trinitrotoluene (common name), or TNT.
Note that the methyl group is individually named due to the exclusion of toluene from the IUPAC nomenclature.

Figure 19. The common name 2,4-dibromophenol, is shared by the IUPAC systematic nomenclature.
Only substituents phenol, benzoic acid, and benzaldehyde share this commonality.
Since the IUPAC nomenclature primarily rely on the simple benzene naming system for the nomenclature of different benzene
derived compounds, the OMP (ortho-, meta-, para-) system is not accepted in the IUPAC nomenclature. For this reason, the OMP
system will yield common names that can be converted to systematic names by using the same method as above. For example, o-
Xylene from the OMP system can be named 1,2-dimethylbenzene by using simple benzene naming (IUPAC standard).

The Phenyl and Benzyl Groups

The Phenyl Group
As mentioned previously, the phenyl group (Ph-R, C6H5-R) can be formed by removing a hydrogen from benzene and attaching a
substituent to where the hydrogen was removed. To this phenomenon, we can name compounds formed this way by applying this
rule: (phenyl + substituent). For example, a chlorine attached in this manner would be named phenyl chloride, and a bromine
attached in this manner would be named phenyl bromide. (See below diagram)

Figure 20. Naming of Phenyl Chloride and Phenyl Bromide

While compounds like these are usually named by simple benzene type naming (chlorobenzene and bromobenzene), the phenyl
group naming is usually applied to benzene rings where a substituent with six or more carbons is attached, such as in the diagram
below.

Figure 21. Diagram of 2-phenyloctane.

Although the diagram above might be a little daunting to understand at first, it is not as difficult as it seems after careful analysis of
the structure is made. By looking for the longest chain in the compound, it should be clear that the longest chain is eight (8) carbons
long (octane, as shown in green) and that a benzene ring is attached to the second position of this longest chain (labeled in red). As
this rule suggests that the benzene ring will act as a function group (a substituent) whenever a substituent of more than six (6)
carbons is attached to it, the name "benzene" is changed to phenyl and is used the same way as any other substituents, such as

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methyl, ethyl, or bromo. Putting it all together, the name can be derived as: 2-phenyloctane (phenyl is attached at the second
position of the longest carbon chain, octane).

The Benzyl Group

The benzyl group (abbv. Bn), similar to the phenyl group, is formed by manipulating the benzene ring. In the case of the benzyl
group, it is formed by taking the phenyl group and adding a CH2 group to where the hydrogen was removed. Its molecular
fragment can be written as C6H5CH2-R, PhCH2-R, or Bn-R. Nomenclature of benzyl group based compounds are very similar to
the phenyl group compounds. For example, a chlorine attached to a benzyl group would simply be called benzyl chloride, whereas
an OH group attached to a benzyl group would simply be called benzyl alcohol.

Figure 22. Benzyl Group Nomenclature

Additionally, other substituents can attach on the benzene ring in the presence of the benzyl group. An example of this can be seen
in the figure below:

Figure 23. Nomenclature of 2,4-difluorobenzyl chloride.

Similar to the base name nomenclature system, the carbon in which the base substituent is attached on the benzene ring is given the
first priority and the rest of the substituents are given the lowest number order possible. Under this consideration, the above
compound can be named: 2,4-difluorobenzyl chloride.

Commonly Named Benzene Compounds Nomenclature Summary Flowchart

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 Summary Flowchart (Figure 24). Summary of nomenclature rules used in commonly benzene derived compounds.
As benzene derived compounds can be extremely complex, only compounds covered in this article and other commonly named
compounds can be named using this flowchart.

Determination of Common and Systematic Names using Flowchart

To demonstrate how this flowchart can be used to name TNT in its common and systematic (IUPAC) name, a replica of the
flowchart with the appropriate flow paths are shown below:

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Outside links
Naming Aromatic Compounds - A good review of the concepts presented above
Naming Aromatic Compounds - Functional groups and compounds formed by different functional groups
Naming Aromatic Compounds - Additional practice problems are available here
Aromatherapy and Aromatic Compounds
Michael Faraday - Discovery of Benzene and History
Wikipedia - Camphor
Medicinal Uses of Camphor
More on Terpenes
Properties of Eugenol
Benzene Aromaticity and Stability
Killing with Syringes: Phenol Injections - Reminisce of the Nazi's "euthanasia" project in Auschwitz
Green Tea Health Benefits - Antioxidant effects of EGCG
Green Tea Nutrient EGCG Blocks Diabetes - Promoting Effects of High Fructose Corn Syrup
Catechins in Green Tea - Why Catechins is Important to Your Health
Phytochemicals - Catechins
Wikipedia - Trinitrotoluene (TNT)
IUPAC Nomenclature System and Recommendations

2.4.9 https://chem.libretexts.org/@go/page/16983
 Wikipedia - Phenyl Group
Wikipedia - Benzyl Group

References
1. Nicolaou, K. C., & Montagnon, T. (2008). Molecules That Changed the World. KGaA, Weinheim: Wiley-VCH. p. 54
2. Pitman, V. (2004). Aromatherapy. Great Britain, UK: Nelson Thornes. p.135-136
3. Burton, G. (2000). Chemical Ideas. Bicester, Oxon: Heinemann. p.290-292
4. Vollhardt, K. P.C. & Shore, N. (2007). Organic Chemistry (5th Ed.). New York: W. H. Freeman. p. 667-669
5. Schnaubelt, K. (1999). Medical Aromatherapy. Berkeley, CA: Frog Books. p. 211-213
6. Patrick, G. L. (2004). Organic Chemistry. New York, NY: Taylor & Francis. p. 135-136
7. Talbott, S. M. (2002). A Guide to Understanding Dietary Supplements. Binghamton, NY: Haworth Press. p. 616-619
8. Lifton, R. J. (2000). The Nazi doctors. New York, NY: Basic Books. p. 255-261
9. Myers, R. L., & Myers, R. L. (2007). The 100 most important chemical compounds. Westport, CT: Greenwood Publishing
Group. p. 281-282

Practice Problems

Q1) (True/False) The compound above contains a benzene ring and thus is aromatic.
Q2) Benzene unusual stability is caused by how many conjugated pi bonds in its cyclic ring? ____
Q3) Menthol, a topical analgesic used in many ointments for the relief of pain, releases a peppermint aroma upon exposure to the
air. Based on this conclusion, can you imply that a benzene ring is present in its chemical structure? Why or why not?

Q4)
Q5) At normal conditions, benzene has ___ resonance structures.
Q6) Which of the following name(s) is/are correct for the following compound?

a) nitrohydride benzene
b) phenylamine
c) phenylamide
d) aniline
e) nitrogenhydrogen benzene
f) All of the above is correct
Q7) Convert 1,4-dimethylbenzene into its common name.
Q8) TNT's common name is: ______________________________
Q9) Name the following compound using OMP nomenclature:

Q10) Draw the structure of 2,4-dinitrotoluene.

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Q11) Name the following compound:

Q12) Which of the following is the correct name for the following compound?

a) 3,4-difluorobenzyl bromide
b) 1,2-difluorobenzyl bromide
c) 4,5-difluorobenzyl bromide
d) 1,2-difluoroethyl bromide
e) 5,6-difluoroethyl bromide
f) 4,5-difluoroethyl bromide
Q13) (True/False) Benzyl chloride can be abbreviated Bz-Cl.
Q14) Benzoic Acid has what R group attached to its phenyl functional group?
Q15) (True/False) A single aromatic compound can have multiple names indicating its structure.
Q16) List the corresponding positions for the OMP system (o-, m-, p-).
Q17) A scientist has conducted an experiment on an unknown compound. He was able to determine that the unknown compound
contains a cyclic ring in its structure as well as an alcohol (-OH) group attached to the ring. What is the unknown compound?
a) Cyclohexanol
b) Cyclicheptanol
c) Phenol
d) Methanol
e) Bleach
f) Cannot determine from the above information
Q18) Which of the following statements is false for the compound, phenol?
a) Phenol is a benzene derived compound.
b) Phenol can be made by attaching an -OH group to a phenyl group.
c) Phenol is highly toxic to the body even in small doses.
d) Phenol can be used as a catalyst in the hydrogenation of benzene into cyclohexane.
e) Phenol is used as an antiseptic in minute doses.
f) Phenol is amongst one of the three common names retained in the IUPAC nomenclature.

Answer Key to Practice Questions

Q1) False, this compound does not contain a benzene ring in its structure.
Q2) 3
Q3) No, a substance that is fragrant does not imply a benzene ring is in its structure. See camphor example (figure 1)
Q4) No reaction, benzene requires a special catalyst to be hydrogenated due to its unusual stability given by its three conjugated pi
bonds.
Q5) 2
Q6) b, d
Q7) p-Xylene
Q8) 2,4,6-trinitrotoluene

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Q9) p-chloronitrobenzene

Q10)
Q11) 4-phenylheptane
Q12) a
Q13) False, the correct abbreviation for the benzyl group is Bn, not Bz. The correct abbreviation for Benzyl chloride is Bn-Cl.
Q14) COOH
Q15) True. TNT, for example, has the common name 2,4,6-trinitrotoluene and its systematic name is 2-methyl-1,3,5-
trinitrobenzene.
Q16) Ortho - 1,2 ; Meta - 1,3 ; Para - 1,4
Q17) The correct answer is f). We cannot determine what structure this is since the question does not tell us what kind of cyclic
ring the -OH group is attached on. Just as cyclohexane can be cyclic, benzene and cycloheptane can also be cyclic.
Q18) d

Contributors
David Lam

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2.5: Functional Groups
Functional groups in organic compounds
Functional groups are structural units within organic compounds that are defined by specific
bonding arrangements between specific atoms. The structure of capsaicin, the compound
discussed in the beginning of this chapter, incorporates several functional groups, labeled in
the figure below and explained throughout this section.

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 behave in organic reactions.
The 'default' in organic chemistry (essentially, the lack of any functional groups) is given the
term alkane, characterized by single bonds between carbon and carbon, or between carbon
and hydrogen. Methane, CH4, is the natural gas you may burn in your furnace. Octane, C8H18,
is a component of gasoline.

Alkanes

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

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In chapter 2, we will study the nature of the bonding on alkenes and alkynes, and learn that that
the bonding in alkenes is trigonal planar in in alkynes is linear. Furthermore, many alkenes can
take two geometric forms: cis or trans. The cis and trans forms of a given alkene are different
molecules with different physical properties because, as we will learn in chapter 2, 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.

We will have more to say about the subject of cis and trans alkenes in chapter 3, and we will
learn much more about the reactivity of alkenes in chapter 14.
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 15, 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 chapters 2 and 14.

Aromatics

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When the carbon of an alkane is bonded to one or more halogens, the group is referred to as a
alkyl halide or haloalkane. 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.
Haloalkanes

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. The sulfur analog
of an alcohol is called a thiol (from the Greek thio, for sulfur).
Alcohols, phenols, and thiols

Note that the definition of a phenol states that the hydroxyl oxygen must be directly attached to
one of the carbons of the aromatic ring. The compound below, therefore, is not a phenol - it is a
primary alcohol.

The distinction is important, because as we will see later, there is a significant difference in the
reactivity of alcohols and phenols.

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The deprotonated forms of alcohols, phenols, and thiols are called alkoxides, phenolates, and
thiolates, respectively. A protonated alcohol is an oxonium ion.

In an ether functional group, a central oxygen is bonded to two carbons. Below is the structure
of diethyl ether, a common laboratory solvent and also one of the first compounds to be used
as an anesthetic during operations. The sulfur analog of an ether is called a thioether or
sulfide.

Ethers and sulfides

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.
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.

Amines

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 Note: 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.

Phosphate and its derivative functional groups are ubiquitous in biomolecules. Phosphate
linked to a single organic group is called a phosphate ester; when it has two links to organic
groups it is called a phosphate diester. A linkage between two phosphates creates a
phosphate anhydride.

Organic phosphates

Chapter 9 of this book is devoted to the structure and reactivity of the phosphate group.
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.
A group with a carbon-nitrogen double bond is called an imine, or sometimes a Schiff base (in
this book we will use the term 'imine'). The chemistry of aldehydes, ketones, and imines will be
covered in chapter 10.

Aldehydes, ketones, and imines

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When a carbonyl carbon is bonded on one side to a carbon (or hydrogen) and on the other side
to an oxygen, nitrogen, or sulfur, the functional group is considered to be one of the ‘carboxylic
acid derivatives’, a designation that describes a set of related functional groups. The
eponymous member of this family is the carboxylic acid functional group, in which the
carbonyl is bonded to a hydroxyl group. The conjugate base of a carboxylic acid is a
carboxylate. Other derivatives are carboxylic esters (usually just called 'esters'), thioesters,
amides, acyl phosphates, acid chlorides, and acid anhydrides. With the exception of acid
chlorides and acid anhydrides, the carboxylic acid derivatives are very common in biological
molecules and/or metabolic pathways, and their structure and reactivity will be discussed in
detail in chapter 11.
Carboxylic acid derivatives

Finally, a nitrile group is characterized by a carbon triple-bonded to a nitrogen.

Nitriles

A single compound often contains several functional groups, particularly in biological organic chemistry. 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’).

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The hormone testosterone, the amino acid phenylalanine, and the glycolysis metabolite
dihydroxyacetone phosphate all contain multiple functional groups, as labeled below.

While not in any way a complete list, this section has covered most of the important functional
groups that we will encounter in biological organic chemistry. Table 9 in the tables section at the
back of this book 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 1.12: Identify the functional groups (other than alkanes) in the following organic
compounds. State whether alcohols and amines are primary, secondary, or tertiary.

Solutions to exercises

Exercise 1.13: Draw one example each 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). There are many

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 possible correct answers for these, so be sure to check your structures with your instructor or
tutor.
a) a compound with molecular formula C6H11NO that includes alkene, secondary amine,
and primary alcohol functional groups
2-
b) an ion with molecular formula C3H5O6P 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.

Naming organic compounds

A system has been devised by the International Union of Pure and Applied Chemistry (IUPAC, usually pronounced
eye-you-pack) for naming organic compounds. While the IUPAC system is convenient for naming relatively small,
simple organic compounds, it is not generally used in the naming of biomolecules, which tend to be quite large and
complex. It is, however, a good idea (even for biologists) to become familiar with the basic structure of the IUPAC
system, and be able to draw simple structures based on their IUPAC names.
Naming an organic compound usually begins with identify what is referred to as the 'parent chain', which is the longest
straight chain of carbon atoms. We’ll start with the simplest straight chain alkane structures. CH4 is called methane,
and C2H6 ethane. The table below continues with the names of longer straight-chain alkanes: be sure to commit these
to memory, as they are the basis for the rest of the IUPAC nomenclature system (and are widely used in naming
biomolecules as well).

Names for straight-chain alkanes:

1 carbon: methane
2 carbons: ethane
3 carbons: propane
4 carbons: butane
5 carbons: pentane
6 carbons: hexane
7 carbons: heptane
8 carbons: octane
9 carbons: nonane
10 carbons: decane

Substituents branching from the main parent chain are located by a carbon number, with the lowest possible numbers
being used (for example, notice in the example below that the compound on the left is named 1-chlorobutane, not 4-
chlorobutane). When the substituents are small alkyl groups, the terms methyl, ethyl, and propyl are used.

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Other common names for hydrocarbon substituent groups isopropyl, tert-butyl and phenyl.

Notice in the example below, an ‘ethyl group’ (in blue) is not treated as a substituent, rather it is included as part of the
parent chain, and the methyl group is treated as a substituent. The IUPAC name for straight-chain hydrocarbons is
always based on the longest possible parent chain, which in this case is four carbons, not three.

Cyclic alkanes are called cyclopropane, cyclobutane, cyclopentane, cyclohexane, and so on:

In the case of multiple substituents, the prefixes di, tri, and tetra are used.

Functional groups have characteristic suffixes. Alcohols, for example, have ‘ol’ appended to the parent chain name,
along with a number designating the location of the hydroxyl group. Ketones are designated by ‘one’.

Alkenes are designated with an 'ene' ending, and when necessary the location and geometry of the double bond are
indicated. Compounds with multiple double bonds are called dienes, trienes, etc.

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Some groups can only be present on a terminal carbon, and thus a locating number is not necessary: aldehydes end in
‘al’, carboxylic acids in ‘oic acid’, and carboxylates in ‘oate’.

Ethers and sulfides are designated by naming the two groups on either side of the oxygen or sulfur.

If an amide has an unsubstituted –NH2 group, the suffix is simply ‘amide’. In the case of a substituted amide, the group
attached to the amide nitrogen is named first, along with the letter ‘N’ to clarify where this group is located. Note that
the structures below are both based on a three-carbon (propan) parent chain.

For esters, the suffix is 'oate'. The group attached to the oxygen is named first.

All of the examples we have seen so far have been simple in the sense that only one functional group was present on
each molecule. There are of course many more rules in the IUPAC system, and as you can imagine, the IUPAC naming
of larger molecules with multiple functional groups, ring structures, and substituents can get very unwieldy very quickly.
The illicit drug cocaine, for example, has the IUPAC name 'methyl (1R,2R,3S,5S)-3-(benzoyloxy)-8-methyl-8-
azabicyclo[3.2.1] octane-2-carboxylate' (this name includes designations for stereochemistry, which is a structural issue
that we will not tackle until chapter 3).

You can see why the IUPAC system is not used very much in biological organic chemistry - the molecules are just too
big and complex. A further complication is that, even outside of a biological context, many simple organic molecules
are known almost universally by their ‘common’, rather than IUPAC names. The compounds acetic acid, chloroform,
and acetone are only a few examples.

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In biochemistry, nonsystematic names (like 'cocaine', 'capsaicin', 'pyruvate' or 'ascorbic acid') are usually used, and
when systematic nomenclature is employed it is often specific to the class of molecule in question: different systems
have evolved, for example, for fats and for carbohydrates. We will not focus very intensively in this text on IUPAC
nomenclature or any other nomenclature system, but if you undertake a more advanced study in organic or biological
chemistry you may be expected to learn one or more naming systems in some detail.

Exercise 1.14: Give IUPAC names for acetic acid, chloroform, and acetone.
Exercise 1.15: Draw line structures of the following compounds, based on what you have learned about the
IUPAC nomenclature system:
a) methylcyclohexane
b) 5-methyl-1-hexanol
c) 2-methyl-2-butene
d) 5-chloropentanal
e) 2,2-dimethylcyclohexanone
f) 4-penteneoic acid
g) N-ethyl-N-cyclopentylbutanamide
Solutions to exercises

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:

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. For example, in chapter 15 when we look at biochemical oxidation-reduction
reactions involving the flavin molecule, we will abbreviate a large part of the flavin structure
which does not change at all in the reactions of interest:

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As an alternative, we can use a 'break' symbol to indicate that we are looking at a small piece or section of a larger
molecule. This is used commonly in the context of drawing groups on large polymers such as proteins or DNA.

Finally, 'R' groups can be used to concisely illustrate a series of related compounds, such as the family of penicillin-
based antibiotics.

Using abbreviations appropriately is a very important skill to develop when studying organic chemistry in a biological
context, because although many biomolecules are very large and complex (and take forever to draw!), usually we are
focusing on just one small part of the molecule where a change is taking place.

As a rule, you should never abbreviate any atom involved in a bond-breaking or bond-forming event that is being
illustrated: only abbreviate that part of the molecule which is not involved in the reaction of interest.

For example, carbon #2 in the reactant/product below most definitely is involved in bonding changes, and therefore
should not be included in the 'R' group.

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Ifyou are unsure whether to draw out part of a structure or abbreviate it, the safest thing to do
is to draw it out.
Exercise 1.16:
a) If you intend to draw out the chemical details of a reaction in which the methyl ester functional group of cocaine
(see earlier figure) was converted to a carboxylate plus methanol, what would be an appropriate abbreviation to use
for the cocaine structure (assuming that you only wanted to discuss the chemistry specifically occurring at the ester
group)?
b) Below is the (somewhat complicated) reaction catalyzed by an enzyme known as 'Rubisco', by which plants 'fix'
carbon dioxide. Carbon dioxide and the oxygen of water are colored red and blue respectively to help you see where
those atoms are incorporated into the products. Propose an appropriate abbreviation for the starting compound
(ribulose 1,5-bisphosphate), using two different 'R' groups, R1 and R2.

Solutions to exercises

Kahn Academy video tutorial on functional groups

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

Further Reading

MasterOrganicChemistry

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Meet the (Most Important) Functional Groups
Carey 4th Edition On-Line Activity
Functional Groups
Khan Academy
Functional Groups Pt 1
Functional Groups Pt 2
Slide Presentations
Functional Group Presentation
Web Pages
Concept Of The Functional Group
Nice Description Of Functional Groups
Purdue Page on Functional Groups
Another Functional Group Overview
CHM 25500 Handout On Functional Groups
Functional Group Overview
Functional Group Review
Videos
Functional Groups (short)
Functional Group Overview Video
Tutorial
Functional Group Flashcards
Another Set Of Flashcards On Functional Groups
Functional Group Handout
Jmol App For Functional Groups
Other Resources
Functional Group Rap

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(perhaps the best link in the entire text)
Practice Problems
Functional Group Quiz
Functional Group Practice
2.5: Functional Groups is shared under a CC BY-NC-SA 4.0 license and was authored, remixed, and/or curated by LibreTexts.

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2.5: Alcohols
Primary alcohols
In a primary (1°) alcohol, the carbon which carries the -OH group is only attached to one alkyl group. Some examples of
primary alcohols include:

Notice that it doesn't matter how complicated the attached alkyl group is. In each case there is only one linkage to an alkyl
group from the CH2 group holding the -OH group. There is an exception to this. Methanol, CH3OH, is counted as a primary
alcohol even though there are no alkyl groups attached to the carbon with the -OH group on it.

Secondary alcohols
In a secondary (2°) alcohol, the carbon with the -OH group attached is joined directly to two alkyl groups, which may be the
same or different. Examples:

Tertiary alcohols
In a tertiary (3°) alcohol, the carbon atom holding the -OH group is attached directly to three alkyl groups, which may be any
combination of same or different. Examples:

Nomenclature
In the IUPAC system of nomenclature, functional groups are normally designated in one of two ways. The presence of the function
may be indicated by a characteristic suffix and a location number. This is common for the carbon-carbon double and triple bonds
which have the respective suffixes ene and yne. Halogens, on the other hand, do not have a suffix and are named as substituents,
for example: (CH3)2C=CHCHClCH3 is 4-chloro-2-methyl-2-pentene. If you are uncertain about the IUPAC rules for nomenclature
you should review them now.
Alcohols are usually named by the first procedure and are designated by an ol suffix, as in ethanol, CH3CH2OH (note that a locator
number is not needed on a two-carbon chain). On longer chains the location of the hydroxyl group determines chain numbering.
For example: (CH3)2C=CHCH(OH)CH3 is 4-methyl-3-penten-2-ol. Other examples of IUPAC nomenclature are shown below,
together with the common names often used for some of the simpler compounds. For the mono-functional alcohols, this common
system consists of naming the alkyl group followed by the word alcohol. Alcohols may also be classified as primary, 1º,
secondary, 2º & tertiary, 3º, in the same manner as alkyl halides. This terminology refers to alkyl substitution of the carbon atom
bearing the hydroxyl group (colored blue in the illustration).

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Many functional groups have a characteristic suffix designator, and only one such suffix (other than "ene" and "yne") may be used
in a name. When the hydroxyl functional group is present together with a function of higher nomenclature priority, it must be cited
and located by the prefix hydroxy and an appropriate number. For example, lactic acid has the IUPAC name 2-hydroxypropanoic
acid.

Contributors
William Reusch, Professor Emeritus (Michigan State U.), Virtual Textbook of Organic Chemistry

2.5: Alcohols is shared under a CC BY-NC-SA 4.0 license and was authored, remixed, and/or curated by LibreTexts.

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2.6: Ethers, Epoxides and Sulfides
Ethers
Ethers are compounds having two alkyl or aryl groups bonded to an oxygen atom, as in the formula R1–O–R2. The ether functional
group does not have a characteristic IUPAC nomenclature suffix, so it is necessary to designate it as a substituent. To do so the
common alkoxy substituents are given names derived from their alkyl component (below):

Alkyl Group Name Alkoxy Group Name

CH3– Methyl CH3O– Methoxy

CH3CH2– Ethyl CH3CH2O– Ethoxy

(CH3)2CH– Isopropyl (CH3)2CHO– Isopropoxy

(CH3)3C– tert-Butyl (CH3)3CO– tert-Butoxy

C6H5– Phenyl C6H5O– Phenoxy

The smaller, shorter alkyl group becomes the alkoxy substituent. The larger, longer alkyl group side becomes the alkane base name.
Each alkyl group on each side of the oxygen is numbered separately. The numbering priority is given to the carbon closest to the
oxgen. The alkoxy side (shorter side) has an "-oxy" ending with its corresponding alkyl group. For example, CH3CH2CH2CH2CH2-
O-CH2CH2CH3 is 1-propoxypentane. If there is cis or trans stereochemistry, the same rule still applies.

Example

Examples are: CH3CH2OCH2CH3, diethyl ether (sometimes referred to as ether), and CH3OCH2CH2OCH3, ethylene glycol dimethyl ether
(glyme).

Common names
Simple ethers are given common names in which the alkyl groups bonded to the oxygen are named in alphabetical order followed
by the word "ether". The top left example shows the common name in blue under the IUPAC name. Many simple ethers are
symmetrical, in that the two alkyl substituents are the same. These are named as "dialkyl ethers".

Epoxides
An epoxide is a cyclic ether with three ring atoms. These rings approximately define an equilateral triangle, which makes it highly
strained. The strained ring makes epoxides more reactive than other ethers. Simple epoxides are named from the parent compound
ethylene oxide or oxirane, such as in chloromethyloxirane. As a functional group, epoxides feature the epoxy prefix, such as in the
compound 1,2-epoxycycloheptane, which can also be called cycloheptene epoxide, or simply cycloheptene oxide.

A generic epoxide.

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The chemical structure of the epoxide glycidol, a common chemical intermediate
A polymer formed by reacting epoxide units is called a polyepoxide or an epoxy. Epoxy resins are used as adhesives and structural
materials. Polymerization of an epoxide gives a polyether, for example ethylene oxide polymerizes to give polyethylene glycol,
also known as polyethylene oxide.

Sulfides (Thioethers)
A thioether is a functional group in organosulfur chemistry with the connectivity C-S-C as shown below. Like many other sulfur-
containing compounds, volatile thioethers have foul odors.[1] A thioether is similar to an ether except that it contains a sulfur atom
in place of the oxygen. The grouping of oxygen and sulfur in the periodic table suggests that the chemical properties of ethers and
thioethers are somewhat similar.

General structure of a thioether with the blue marked functional group.

Nomenclature
Thioethers are sometimes called sulfides, especially in the older literature and this term remains in use for the names of specific
thioethers. The two organic substituents are indicated by the prefixes. (CH3)2S is called dimethylsulfide. Some thioethers are
named by modifying the common name for the corresponding ether. For example, C6H5SCH3 is methyl phenyl sulfide, but is more
commonly called thioanisole, since its structure is related to that for anisole, C6H5OCH3.

Structure and properties

Thioether is an angular functional group, the C-S-C angle approaching 90°. The C-S bonds are about 180 pm.
Thioethers are characterized by their strong odors, which are similar to thiol odor. This odor limits the applications of volatile
thioethers. In terms of their physical properties they resemble ethers but are less volatile, higher melting, and less hydrophilic.
These properties follow from the polarizability of the divalent sulfur center, which is greater than that for oxygen in ethers.

Thiophenes
Thiophenes are a special class of thioether-containing heterocyclic compounds. Because of their aromatic character, they are non-
nucleophilic. The nonbonding electrons on sulfur are delocalized into the π-system. As a consequence, thiophene exhibits few
properties expected for a thioether - thiophene is non-nucleophilic at sulfur and, in fact, is sweet-smelling. Upon hydrogenation,
thiophene gives tetrahydrothiophene, C4H8S, which indeed does behave as a typical thioether.

Contributors
Wikipedia (used with permission)

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2.7: Amines
In the IUPAC system of nomenclature, functional groups are normally designated in one of two ways. The presence of the function
may be indicated by a characteristic suffix and a location number. This is common for the carbon-carbon double and triple bonds
which have the respective suffixes ene and yne. Halogens, on the other hand, do not have a suffix and are named as substituents,
for example: (CH3)2C=CHCHClCH3 is 4-chloro-2-methyl-2-pentene. If you are uncertain about the IUPAC rules for nomenclature
you should review them now.
Amines are derivatives of ammonia in which one or more of the hydrogens has been replaced by an alkyl or aryl group. The
nomenclature of amines is complicated by the fact that several different nomenclature systems exist, and there is no clear
preference for one over the others. Furthermore, the terms primary (1º), secondary (2º) & tertiary (3º) are used to classify amines in
a completely different manner than they were used for alcohols or alkyl halides. When applied to amines these terms refer to the
number of alkyl (or aryl) substituents bonded to the nitrogen atom, whereas in other cases they refer to the nature of an alkyl
group. The four compounds shown in the top row of the following diagram are all C4H11N isomers. The first two are classified as
1º-amines, since only one alkyl group is bonded to the nitrogen; however, the alkyl group is primary in the first example and
tertiary in the second. The third and fourth compounds in the row are 2º and 3º-amines respectively. A nitrogen bonded to four
alkyl groups will necessarily be positively charged, and is called a 4º-ammonium cation. For example, (CH3)4N(+) Br(–) is
tetramethylammonium bromide.

The IUPAC names are listed first and colored blue. This system names amine functions as substituents on the largest alkyl
group. The simple -NH substituent found in 1º-amines is called an amino group. For 2º and 3º-amines a compound prefix (e.g.
dimethylamino in the fourth example) includes the names of all but the root alkyl group.
The Chemical Abstract Service has adopted a nomenclature system in which the suffix -amine is attached to the root alkyl
name. For 1º-amines such as butanamine (first example) this is analogous to IUPAC alcohol nomenclature (-ol suffix). The
additional nitrogen substituents in 2º and 3º-amines are designated by the prefix N- before the group name. These CA names are
colored magenta in the diagram.
Finally, a common system for simple amines names each alkyl substituent on nitrogen in alphabetical order, followed by the
suffix -amine. These are the names given in the last row (colored black).
Many aromatic and heterocyclic amines are known by unique common names, the origins of which are often unknown to the
chemists that use them frequently. Since these names are not based on a rational system, it is necessary to memorize them. There is
a systematic nomenclature of heterocyclic compounds, but it will not be discussed here.

Contributors
William Reusch, Professor Emeritus (Michigan State U.), Virtual Textbook of Organic Chemistry

2.7: Amines is shared under a CC BY-NC-SA 4.0 license and was authored, remixed, and/or curated by LibreTexts.

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2.8: Aldehydes and Ketones
Aldehydes and ketones contain the carbonyl group. Aldehydes are considered the most important functional group. They are often
called the formyl or methanoyl group. Aldehydes derive their name from the dehydration of alcohols. Aldehydes contain the
carbonyl group bonded to at least one hydrogen atom. Ketones contain the carbonyl group bonded to two carbon atoms.
Aldehydes and ketones are organic compounds which incorporate a carbonyl functional group, C=O. The carbon atom of this
group has two remaining bonds that may be occupied by hydrogen, alkyl or aryl substituents. If at least one of these substituents is
hydrogen, the compound is an aldehyde. If neither is hydrogen, the compound is a ketone.

Naming Aldehydes
The IUPAC system of nomenclature assigns a characteristic suffix -al to aldehydes. For example, H2C=O is methanal, more
commonly called formaldehyde. Since an aldehyde carbonyl group must always lie at the end of a carbon chain, it is always is
given the #1 location position in numbering and it is not necessary to include it in the name. There are several simple carbonyl
containing compounds which have common names which are retained by IUPAC.
Also, there is a common method for naming aldehydes and ketones. For aldehydes common parent chain names, similar to those
used for carboxylic acids, are used and the suffix –aldehyde is added to the end. In common names of aldehydes, carbon atoms
near the carbonyl group are often designated by Greek letters. The atom adjacent to the carbonyl function is alpha, the next
removed is beta and so on.

If the aldehyde moiety (-CHO) is attached to a ring the suffix –carbaldehyde is added to the name of the ring. The carbon
attached to this moiety will get the #1 location number in naming the ring.

 Summary of Aldehyde Nomenclature rules

1. Aldehydes take their name from their parent alkane chains. The -e is removed from the end and is replaced with -al.
2. The aldehyde funtional group is given the #1 numbering location and this number is not included in the name.
3. For the common name of aldehydes start with the common parent chain name and add the suffix -aldehyde. Substituent
positions are shown with Greek letters.
4. When the -CHO functional group is attached to a ring the suffix -carbaldehyde is added, and the carbon attached to that
group is C1.

 Example 1

The IUPAC system names are given on top while the common name is given on the bottom in parentheses.

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Aldehyde Common Names to Memorize

There are some common names that are still used and need to be memorized. Recognizing the
patterns can be helpful.

Naming Ketones
The IUPAC system of nomenclature assigns a characteristic suffix of -one to ketones. A ketone carbonyl function may be located
anywhere within a chain or ring, and its position is usually given by a location number. Chain numbering normally starts from the
end nearest the carbonyl group. Very simple ketones, such as propanone and phenylethanone do not require a locator number, since
there is only one possible site for a ketone carbonyl function. The common names for ketones are formed by naming both alkyl
groups attached to the carbonyl then adding the suffix -ketone. The attached alkyl groups are arranged in the name alphabetically.

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  Summary of Ketone Nomenclature rules
1. Ketones take their name from their parent alkane chains. The ending -e is removed and replaced with -one.
2. The common name for ketones are simply the substituent groups listed alphabetically + ketone.
3. Some common ketones are known by their generic names. Such as the fact that propanone is commonly referred to as
acetone.

 Example 2

The IUPAC system names are given on top while the common name is given on the bottom in parentheses.

Ketone Common Names to Memorize

There are some common names that are still used and need to be memorized. Recognizing the
patterns can be helpful.

Naming Aldehydes and Ketones in the Same Molecule

As with many molecules with two or more functional groups, one is given priority while the other is named as a substituent.
Because aldehydes have a higher priority than ketones, molecules which contain both functional groups are named as aldehydes
and the ketone is named as an "oxo" substituent. It is not necessary to give the aldehyde functional group a location number,
however, it is usually necessary to give a location number to the ketone.

 Example 3

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Naming Dialdehydes and Diketones
For dialdehydes the location numbers for both carbonyls are omitted because the aldehyde functional groups are expected to
occupy the ends of the parent chain. The ending –dial is added to the end of the parent chain name.

 Example 4

For diketones both carbonyls require a location number. The ending -dione or -dial is added to the end of the parent chain.

 Example 5

Naming Cyclic Ketones and Diketones

In cyclic ketones the carbonyl group is assigned location position #1, and this number is not included in the name, unless more than
one carbonyl group is present. The rest of the ring is numbered to give substituents the lowest possible location numbers.
Remember the prefix cyclo is included before the parent chain name to indicate that it is in a ring. As with other ketones the –e
ending is replaced with the –one to indicate the presence of a ketone.
With cycloalkanes which contain two ketones both carbonyls need to be given a location numbers. Also, an –e is not removed from
the end, but the suffix –dione is added.

 Example 6

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Naming Carbonyls and Hydroxyls in the Same
Molecule
When and aldehyde or ketone is present in a molecule which also contains an alcohol functional group the carbonyl is given
nomenclature priority by the IUPAC system. This means that the carbonyl is given the lowest possible location number and the
appropriate nomenclature suffix is included. In the case of alcohols the OH is named as a hydroxyl substituent. However, the l in
hydroxyl is generally removed.

 Example 7

Naming Carbonyls and Alkenes in the Same Molecule

When and aldehyde or ketone is present in a molecule which also contains analkene functional group the carbonyl is given
nomenclature priority by the IUPAC system. This means that the carbonyl is given the lowest possible location number and the
appropriate nomenclature suffix is included. When carbonyls are included with an alkene the following order is followed:
(Location number of the alkene)-(Prefix name for the longest carbon chain minus the -ane ending)-(an -en ending to indicate the
presence of an alkene)-(the location number of the carbonyl if a ketone is present)-(either an –one or and -anal ending).

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Remember that the carbonyl has priority so it should get the lowest possible location number. Also, remember that cis/tran or E/Z
nomenclature for the alkene needs to be included if necessary.

 Example 8

Aldehydes and Ketones as Fragments

Alkanoyl is the common name of the fragment, though the older naming, acyl, is still widely used.
Formyl is the common name of the fragment.
Acety is the common name of the CH3-C=O- fragment.

 Example 9

Additional Examples of Carbonyl Nomenclature

1) Please give the IUPAC name for each compound:

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Answers for Question 1
A. 3,4-dimethylhexanal
B. 5-bromo-2-pentanone
C. 2,4-hexanedione
D. cis-3-pentenal (or (Z)-3-pentenal)
E. 6-methyl-5-hepten-3-one
F. 3-hydroxy-2,4-pentanedione
G. 1,2-cyclobutanedione
H. 2-methyl-propanedial
I. 3-methyl-5-oxo-hexanal
J. cis-2,3-dihydroxycyclohexanone
K. 3-bromo-2-methylcyclopentanecarboaldehyde
L. 3-bromo-2-methylpropanal
2) Please give the structure corresponding to each name:
A) butanal
B) 2-hydroxycyclopentanone
C) 2,3-pentanedione
D) 1,3-cyclohexanedione
E) 4-hydoxy-3-methyl-2-butanone

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F) (E) 3-methyl-2-hepten-4-one
G) 3-oxobutanal
H) cis-3-bromocyclohexanecarboaldehyde
I) butanedial
J) trans-2-methyl-3-hexenal
Answers to question 2:

References
1. Vollhardt, K. Peter C., and Neil E. Schore. Organic Chemistry. 5th ed. New York: W.H. Freeman, 2007.
2. Zumdahl, Steven S., and Susan A. Zumdahl. Chemistry. 6th ed. Boston: Houghton Mifflin College Division, 2002.

Contributors
Prof. Steven Farmer (Sonoma State University)
William Reusch, Professor Emeritus (Michigan State U.), Virtual Textbook of Organic Chemistry

2.8: Aldehydes and Ketones is shared under a CC BY-NC-SA 4.0 license and was authored, remixed, and/or curated by LibreTexts.
Nomenclature of Aldehydes & Ketones is licensed CC BY-NC-SA 4.0.

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2.9: Carboxylic Acids
The IUPAC system of nomenclature assigns a characteristic suffix to these classes. The –e ending is removed from the name of the
parent chain and is replaced -anoic acid. Since a carboxylic acid group must always lie at the end of a carbon chain, it is always is
given the #1 location position in numbering and it is not necessary to include it in the name.
Many carboxylic acids are called by the common names. These names were chosen by chemists to usually describe a source of
where the compound is found. In common names of aldehydes, carbon atoms near the carboxyl group are often designated by
Greek letters. The atom adjacent to the carbonyl function is alpha, the next removed is beta and so on.

Formula Common Name Source IUPAC Name Melting Point Boiling Point

HCO2H formic acid ants (L. formica) methanoic acid 8.4 ºC 101 ºC

CH3CO2H acetic acid vinegar (L. acetum) ethanoic acid 16.6 ºC 118 ºC

milk (Gk. protus

CH3CH2CO2H propionic acid propanoic acid -20.8 ºC 141 ºC
prion)

CH3(CH2)2CO2H butyric acid butter (L. butyrum) butanoic acid -5.5 ºC 164 ºC

CH3(CH2)3CO2H valeric acid valerian root pentanoic acid -34.5 ºC 186 ºC

CH3(CH2)4CO2H caproic acid goats (L. caper) hexanoic acid -4.0 ºC 205 ºC

CH3(CH2)5CO2H enanthic acid vines (Gk. oenanthe) heptanoic acid -7.5 ºC 223 ºC

CH3(CH2)6CO2H caprylic acid goats (L. caper) octanoic acid 16.3 ºC 239 ºC

CH3(CH2)7CO2H pelargonic acid pelargonium (an herb) nonanoic acid 12.0 ºC 253 ºC

CH3(CH2)8CO2H capric acid goats (L. caper) decanoic acid 31.0 ºC 219 ºC

Example (Common Names Are in Red)

Naming carboxyl groups added to a ring

When a carboxyl group is added to a ring the suffix -carboxylic acid is added to the name of the cyclic compound. The ring carbon
attached to the carboxyl group is given the #1 location number.

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Naming carboxylates
Salts of carboxylic acids are named by writing the name of the cation followed by the name of the acid with the –ic acid ending
replaced by an –ate ending. This is true for both the IUPAC and Common nomenclature systems.

Naming carboxylic acids which contain other functional groups

Carboxylic acids are given the highest nomenclature priority by the IUPAC system. This means that the carboxyl group is given the
lowest possible location number and the appropriate nomenclature suffix is included. In the case of molecules containing
carboxylic acid and alcohol functional groups the OH is named as a hydroxyl substituent. However, the l in hydroxyl is generally
removed.

In the case of molecules containing a carboxylic acid and aldehydes and/or ketones functional groups the carbonyl is named as a
"Oxo" substituent.

In the case of molecules containing a carboxylic acid an amine functional group the amine is named as an "amino" substituent.

When carboxylic acids are included with an alkene the following order is followed:
(Location number of the alkene)-(Prefix name for the longest carbon chain minus the -ane ending)-(an –enoic acid ending to
indicate the presence of an alkene and carboxylic acid)
Remember that the carboxylic acid has priority so it should get the lowest possible location number. Also, remember that cis/tran or
E/Z nomenclature for the alkene needs to be included if necessary.

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Naming dicarboxylic acids
For dicarboxylic acids the location numbers for both carboxyl groups are omitted because both functional groups are expected to
occupy the ends of the parent chain. The ending –dioic acid is added to the end of the parent chain.

Contributors
Prof. Steven Farmer (Sonoma State University)
William Reusch, Professor Emeritus (Michigan State U.), Virtual Textbook of Organic Chemistry

2.9: Carboxylic Acids is shared under a CC BY-NC-SA 4.0 license and was authored, remixed, and/or curated by LibreTexts.

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2.10: Esters, Amides, Acid Halides, Anhydrides and Nitriles
The important classes of organic compounds known as alcohols, phenols, ethers, amines and halides consist of alkyl and/or aryl
groups bonded to hydroxyl, alkoxyl, amino and halo substituents respectively. If these same functional groups are attached to an
acyl group (RCO–) their properties are substantially changed, and they are designated as carboxylic acid derivatives. Carboxylic
acids have a hydroxyl group bonded to an acyl group, and their functional derivatives are prepared by replacement of the hydroxyl
group with substituents, such as halo, alkoxyl, amino and acyloxy. Some examples of these functional derivatives were displayed
earlier.
The following table lists some representative derivatives and their boiling points. An aldehyde and ketone of equivalent molecular
weight are also listed for comparison. Boiling points are given for 760 torr (atmospheric pressure), and those listed as a range are
estimated from values obtained at lower pressures. As noted earlier, the relatively high boiling point of carboxylic acids is due to
extensive hydrogen bonded dimerization. Similar hydrogen bonding occurs between molecules of 1º and 2º-amides (amides having
at least one N–H bond), and the first three compounds in the table serve as hydrogen bonding examples.
Physical Properties of Some Carboxylic Acid Derivatives
Formula IUPAC Name Molecular Weight Boiling Point Water Solubility

CH3(CH2)2CO2H butanoic acid 88 164 ºC very soluble

CH3(CH2)2CONH2 butanamide 87 216-220 ºC soluble

CH3CH2CONHCH3 N-methylpropanamide 87 205 -210 ºC soluble

CH3CON(CH3)2 N,N-dimethylethanamide 87 166 ºC very soluble

HCON(CH3)CH2CH3 N-ethyl, N-methylmethanamide 87 170-180 ºC very soluble

CH3(CH2)3CN pentanenitrile 83 141 ºC slightly soluble

ethanoic methanoic
CH3CO2CHO 88 105-112 ºC reacts with water
anhydride

CH3CH2CO2CH3 methyl propanoate 88 80 ºC slightly soluble

CH3CO2C2H5 ethyl ethanoate 88 77 ºC moderately soluble

CH3CH2COCl propanoyl chloride 92.5 80 ºC reacts with water

CH3(CH2)3CHO pentanal 86 103 ºC slightly soluble

CH3(CH2)2COCH3 2-pentanone 86 102 ºC slightly soluble

The last nine entries in the above table cannot function as hydrogen bond donors, so hydrogen bonded dimers and aggregates are
not possible. The relatively high boiling points of equivalent 3º-amides and nitriles are probably due to the high polarity of these
functions. Indeed, if hydrogen bonding is not present, the boiling points of comparable sized compounds correlate reasonably well
with their dipole moments.

2. Nomenclature
Three examples of acyl groups having specific names were noted earlier. These are often used in common names of compounds. In
the following examples the IUPAC names are color coded, and common names are given in parentheses.
• Esters: The alkyl group is named first, followed by a derived name for the acyl group, the oic or ic suffix in the acid name is
replaced by ate.
e.g. CH3(CH2)2CO2C2H5 is ethyl butanoate (or ethyl butyrate).
Cyclic esters are called lactones. A Greek letter identifies the location of the alkyl oxygen relative to the carboxyl carbonyl group.
• Acid Halides: The acyl group is named first, followed by the halogen name as a separate word.
e.g. CH3CH2COCl is propanoyl chloride (or propionyl chloride).
• Anhydrides: The name of the related acid(s) is used first, followed by the separate word "anhydride".
e.g. (CH3(CH2)2CO)2O is butanoic anhydride & CH3COOCOCH2CH3 is ethanoic propanoic anhydride (or acetic propionic
anhydride).

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• Amides: The name of the related acid is used first and the oic acid or ic acid suffix is replaced by amide (only for 1º-amides).
e.g. CH3CONH2 is ethanamide (or acetamide).
2º & 3º-amides have alkyl substituents on the nitrogen atom. These are designated by "N-alkyl" term(s) at the beginning of the
name.
e.g. CH3(CH2)2CONHC2H5 is N-ethylbutanamide; & HCON(CH3)2 is N,N-dimethylmethanamide (or N,N-dimethylformamide).
Cyclic amides are called lactams. A Greek letter identifies the location of the nitrogen on the alkyl chain relative to the carboxyl
carbonyl group.
• Nitriles: Simple acyclic nitriles are named by adding nitrile as a suffix to the name of the corresponding alkane (same number of
carbon atoms).
Chain numbering begins with the nitrile carbon . Commonly, the oic acid or ic acid ending of the corresponding carboxylic acid is
replaced by onitrile.
A nitrile substituent, e.g. on a ring, is named carbonitrile.
e.g. (CH3)2CHCH2C≡N is 3-methylbutanenitrile (or isovaleronitrile).

Contributors
William Reusch, Professor Emeritus (Michigan State U.), Virtual Textbook of Organic Chemistry

This page titled 2.10: Esters, Amides, Acid Halides, Anhydrides and Nitriles is shared under a CC BY-NC-SA 4.0 license and was authored,
remixed, and/or curated by William Reusch.

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Appendix - IUPAC Nomenclature Rules
Wikipedia Summary
Full Text of IUPAC Rules
Nomenclature 101

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 CHAPTER OVERVIEW

Chapter 3. Stereochemistry

Purdue CHM 26505: Organic

Chemistry for Chemistry Majors (1st
Semester)
Fall 2014: Prof. Mark Lipton

Template:HideTOC

Topic hierarchy
3.1 Stereoisomerism
3.2 Conformations of Alkanes
3.3 Conformation of Cyclohexane
3.4 Chirality
3.5 Enantiomers
3.6 Cahn-Ingold Prelog Rules
3.7 Diastereomers
3.8 Meso Isomers
3.9 Cis/Trans Isomerism

Chapter 3. Stereochemistry is shared under a CC BY-NC-SA 4.0 license and was authored, remixed, and/or curated by LibreTexts.

1
3.1 Stereoisomerism
As defined in an earlier introductory section, isomers are different compounds that have the same molecular formula. When the
group of atoms that make up the molecules of different isomers are bonded together in fundamentally different ways, we refer to
such compounds as constitutional isomers. For example, in the case of the C4H8 hydrocarbons, most of the isomers are
constitutional. Shorthand structures for four of these isomers are shown below with their IUPAC names.

Note that the twelve atoms that make up these isomers are connected or bonded in very different ways. As is true for all
constitutional isomers, each different compound has a different IUPAC name. Furthermore, the molecular formula provides
information about some of the structural features that must be present in the isomers. Since the formula C4H8 has two fewer
hydrogens than the four-carbon alkane butane (C4H10), all the isomers having this composition must incorporate either a ring or a
double bond. A fifth possible isomer of formula C4H8 is CH3CH=CHCH3. This would be named 2-butene according to the IUPAC
rules; however, a close inspection of this molecule indicates it has two possible structures. These isomers may be isolated as
distinct compounds, having characteristic and different properties. They are shown here with the designations cis and trans.

The bonding patterns of the atoms in these two isomers are essentially equivalent, the only difference being the relative orientation
or configuration of the two methyl groups (and the two associated hydrogen atoms) about the double bond. In the cis isomer the
methyl groups are on the same side; whereas they are on opposite sides in the trans isomer. Isomers that differ only in the spatial
orientation of their component atoms are called stereoisomers. Stereoisomers always require that an additional nomenclature
prefix be added to the IUPAC name in order to indicate their spatial orientation, for example, cis (Latin, meaning on this side) and
trans (Latin, meaning across) in the 2-butene case.

Contributors
William Reusch, Professor Emeritus (Michigan State U.), Virtual Textbook of Organic Chemistry

Further Reading

Khan Academy
Stereoisomers, etc.

Websites
Stereoisomerism
Stereoisomer examples
3.1 Stereoisomerism is shared under a CC BY-NC-SA 4.0 license and was authored, remixed, and/or curated by LibreTexts.
Stereoisomers by William Reusch is licensed CC BY-NC-SA 4.0.

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

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

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

The six carbon-hydrogen bonds are shown as solid lines protruding from the two carbons at 120°angles, which is what the actual
tetrahedral geometry looks like when viewed from this perspective and flattened into two dimensions.
The lowest energy conformation of ethane, shown in the figure above, is called the ‘staggered’ conformation, in which all of the C-
H bonds on the front carbon are positioned at dihedral angles of 60°relative to the C-H bonds on the back carbon. In this
conformation, the distance between the bonds (and the electrons in them) is maximized.
If we now rotate the front CH3 group 60°clockwise, the molecule is in the highest energy ‘eclipsed' conformation, where the
hydrogens on the front carbon are as close as possible to the hydrogens on the back carbon.

This is the highest energy conformation because of unfavorable interactions between the electrons in the front and back C-H bonds.
The energy of the eclipsed conformation is approximately 3 kcal/mol higher than that of the staggered conformation.
Another 60°rotation returns the molecule to a second eclipsed conformation. This process can be continued all around the
360°circle, with three possible eclipsed conformations and three staggered conformations, in addition to an infinite number of
variations in between.
The carbon-carbon bond is not completely free to rotate – there is indeed a small, 3 kcal/mol barrier to rotation that must be
overcome for the bond to rotate from one staggered conformation to another. This rotational barrier is not high enough to prevent
constant rotation except at extremely cold temperatures. However, at any given moment the molecule is more likely to be in a
staggered conformation - one of the rotational ‘energy valleys’ - than in any other state.
The potential energy associated with the various conformations of ethane varies with the dihedral angle of the bonds, as shown
below.

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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

Butane Conformations
The hydrocarbon butane has a larger and more complex set of conformations associated with its constitution than does ethane. Of
particular interest and importance are the conformations produced by rotation about the central carbon-carbon bond. Among these
we shall focus on two staggered conformers (A & C) and two eclipsed conformers (B & D), shown below in several stereo-
representations.

As in the case of ethane, the staggered conformers are more stable than the eclipsed conformers by 2.8 to 4.5 kcal/mol. Since the
staggered conformers represent the chief components of a butane sample they have been given the identifying prefix designations
anti for A and gauche for C.
The following diagram illustrates the change in potential energy that occurs with rotation about the C2–C3 bond.

Here is a summary of the most important aspects of conformational stereoisomerism:

(i) Most conformational interconversions in simple molecules occur rapidly at room temperature. Consequently, isolation of
pure conformers is usually not possible.
(ii) Specific conformers require special nomenclature terms such as staggered, eclipsed, gauche and anti when they are
designated.
(iii) Specific conformers may also be designated by dihedral angles. In the butane conformers shown above, the dihedral
angles formed by the two methyl groups about the central double bond are: A 180º, B 120º, C 60º & D 0º.
(iv) Staggered conformations about carbon-carbon single bonds are more stable (have a lower potential energy) than the
corresponding eclipsed conformations. The higher energy of eclipsed bonds is known as eclipsing strain.
(v) In butane the gauche-conformer is less stable than the anti-conformer by about 0.9 kcal/mol. This is due to a crowding of
the two methyl groups in the gauche structure, and is called steric strain or steric hindrance.

Further Reading
Slide presentation on alkane conformations

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Conformational Analysis Problems
Conformation tutorial questions
Conformation of Ethane

Carey 4th Edition On-Line Activity

Conformations of simple alkanes

Khan Academy
Conformations of ethane
Newman Projections

MasterOrganicChemistry
On Cats: Newman Projections

Carey 4th Edition On-Line Activity

Newman Projections

Khan Academy
Newman Projections
Newman Projections 2

Leah4Sci
Newman Projections

Web Pages
Dihedral Angles

Videos
Bond rotations
Newman Projections

Tutorial
How to Draw Newman Projections
Long Newman projection tutorial
Interactive Tutorial

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How to draw Newman projections
Switching between Newman projections and dash-wedge drawings

Other tools
Interactive page on Newman projections
3.2 Conformations of Alkanes is shared under a CC BY-NC-SA 4.0 license and was authored, remixed, and/or curated by LibreTexts.

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3.3 Conformation of Cyclohexane
Although the customary line drawings of simple cycloalkanes are geometrical polygons, the actual shape of these compounds in
most cases is very different.

Cyclopropane is necessarily planar (flat), with the carbon atoms at the corners of an equilateral triangle. The 60º bond angles are
much smaller than the optimum 109.5º angles of a normal tetrahedral carbon atom, and the resulting angle strain dramatically
influences the chemical behavior of this cycloalkane. Cyclopropane also suffers substantial eclipsing strain, since all the carbon-
carbon bonds are fully eclipsed. Cyclobutane reduces some bond-eclipsing strain by folding (the out-of-plane dihedral angle is
about 25º), but the total eclipsing and angle strain remains high. Cyclopentane has very little angle strain (the angles of a pentagon
are 108º), but its eclipsing strain would be large (about 10 kcal/mol) if it remained planar. Consequently, the five-membered ring
adopts non-planar puckered conformations whenever possible.
Rings larger than cyclopentane would have angle strain if they were planar. However, this strain, together with the eclipsing strain
inherent in a planar structure, can be relieved by puckering the ring. Cyclohexane is a good example of a carbocyclic system that
virtually eliminates eclipsing and angle strain by adopting non-planar conformations. Cycloheptane and cyclooctane have greater
strain than cyclohexane, in large part due to transannular crowding (steric hindrance by groups on opposite sides of the ring).

Conformations of Cyclohexane
A planar structure for cyclohexane is clearly improbable. The bond angles would necessarily be 120º, 10.5º larger than the ideal
tetrahedral angle. Also, every carbon-carbon bond in such a structure would be eclipsed. The resulting angle and eclipsing strains
would severely destabilize this structure. If two carbon atoms on opposite sides of the six-membered ring are lifted out of the plane
of the ring, much of the angle strain can be eliminated.

This boat structure still has two eclipsed bonds and severe steric crowding of two hydrogen atoms on the "bow" and "stern" of the
boat. This steric crowding is often called steric hindrance. By twisting the boat conformation, the steric hindrance can be partially
relieved, but the twist-boat conformer still retains some of the strains that characterize the boat conformer. Finally, by lifting one
carbon above the ring plane and the other below the plane, a relatively strain-free 'chair' conformer is formed. This is the
predominant structure adopted by molecules of cyclohexane.
Investigations concerning the conformations of cyclohexane were initiated by H. Sachse (1890) and E. Mohr (1918), but it was not
until 1950 that a full treatment of the manifold consequences of interconverting chair conformers and the different orientations of
pendent bonds was elucidated by D. H. R. Barton (Nobel Prize 1969 together with O. Hassel). The following discussion presents
some of the essential features of this conformational analysis.
On careful examination of a chair conformation of cyclohexane, we find that the twelve hydrogens are not structurally equivalent.
Six of them are located about the periphery of the carbon ring, and are termed equatorial. The other six are oriented above and
below the approximate plane of the ring (three in each location), and are termed axial because they are aligned parallel to the
symmetry axis of the ring.

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In the figure above, the equatorial hydrogens are colored blue, and the axial hydrogens are in bold. Since there are two equivalent
chair conformations of cyclohexane in rapid equilibrium, all twelve hydrogens have 50% equatorial and 50% axial character. The
figure below illustrates how to convert a molecular model of cyclohexane between two different chair conformations - this is
something that you should practice with models. Notice that a 'ring flip' causes equatorial hydrogens to become axial, and vice-
versa.

Because axial bonds are parallel to each other, substituents larger than hydrogen generally suffer greater steric crowding when they
are oriented axial rather than equatorial. Consequently, substituted cyclohexanes will preferentially adopt conformations in which
the larger substituents assume equatorial orientation.

When the methyl group in the structure above occupies an axial position it suffers steric crowding by the two axial hydrogens
located on the same side of the ring.

The conformation in which the methyl group is equatorial is more stable, and thus the equilibrium lies in this direction.
The relative steric hindrance experienced by different substituent groups oriented in an axial versus equatorial location on
cyclohexane may be determined by the conformational equilibrium of the compound. The corresponding equilibrium constant is
related to the energy difference between the conformers, and collecting such data allows us to evaluate the relative tendency of
substituents to exist in an equatorial or axial location.A table of these free energy values (sometimes referred to as A values) may
be examined by clicking here.
Looking at the energy values in this table, it is clear that the apparent "size" of a substituent (in terms of its preference for
equatorial over axial orientation) is influenced by its width and bond length to cyclohexane, as evidenced by the fact that an axial
vinyl group is less hindered than ethyl, and iodine slightly less than chlorine.
We noted earlier that cycloalkanes having two or more substituents on different ring carbon atoms exist as a pair (sometimes more)
of configurational stereoisomers. Now we must examine the way in which favorable ring conformations influence the properties of

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the configurational isomers. Remember, configurational stereoisomers are stable and do not easily interconvert, whereas,
conformational isomers normally interconvert rapidly. In examining possible structures for substituted cyclohexanes, it is useful to
follow two principles:
(i) Chair conformations are generally more stable than other possibilities.
(ii) Substituents on chair conformers prefer to occupy equatorial positions due to the increased steric hindrance of axial
locations.
The following equations and formulas illustrate how the presence of two or more substituents on a cyclohexane ring perturbs the
interconversion of the two chair conformers in ways that can be predicted.
In the case of 1,1-disubstituted cyclohexanes, one of the substituents must necessarily be axial and the other equatorial, regardless
of which chair conformer is considered. Since the substituents are the same in 1,1-dimethylcyclohexane, the two conformers are
identical and present in equal concentration. In 1-t-butyl-1-methylcyclohexane the t-butyl group is much larger than the methyl,
and that chair conformer in which the larger group is equatorial will be favored in the equilibrium( > 99%). Consequently, the
methyl group in this compound is almost exclusively axial in its orientation.

In the cases of 1,2-, 1,3- and 1,4-disubstituted compounds the analysis is a bit more complex. It is always possible to have both
groups equatorial, but whether this requires a cis-relationship or a trans-relationship depends on the relative location of the
substituents. As we count around the ring from carbon #1 to #6, the uppermost bond on each carbon changes its orientation from
equatorial (or axial) to axial (or equatorial) and back. It is important to remember that the bonds on a given side of a chair ring-
conformation always alternate in this fashion. Therefore, it should be clear that for cis-1,2-disubstitution, one of the substituents
must be equatorial and the other axial; in the trans-isomer both may be equatorial. Because of the alternating nature of equatorial
and axial bonds, the opposite relationship is true for 1,3-disubstitution (cis is all equatorial, trans is equatorial/axial).

Finally, 1,4-disubstitution reverts to the 1,2-pattern:

The above analysis is not something that you should try to memorize: rather, become comfortable with drawing cyclohexane in the
chair conformation, with bonds pointing in the correct directions for axial and equatorial substituents. If you can draw a structure
correctly in the chair conformation, you should always be able to determine which positions are axial and which are equatorial.

Further Reading on Cyclohexanes

MasterOrganicChemistry
The ups and downs of cyclohexanes

Carey 4th Edition On-Line Activity

Conformations of Cyclohexanes

Khan Academy
Conformation of cyclohexane I: Chair and Boat

Web Pages
Boat and Chair cyclohexanes

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GOOD Extensive information about cyclohexane conformations

Videos
Chair conformations
Axial vs Equitorial Position pt 1
Axial vs Equitorial Position pt 2

Tutorial
All About Chair Conformations
Drawing Chairs in 3D
Axial and Equitorial positions in cyclohexanes
Drawing Chair conformations
Viewing and Drawing Chair conformations
Conformations of monosubstituted cyclohexanes

Carey 4th Edition On-Line Activity

Conformations of Substituted Cyclohexanes

Khan Academy
Conformation of Cyclohexane II: Monosubstituted

Web Pages
Axial vs Equitorial Exchange

Cis/Trans Isomers of Rings

Cliffs Notes
Cycloalkane stereochemistry

Slide Presentations
Cis- and trans-substituted of cyclohexane

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Conformations of Disubstituted Cyclohexanes

Khan Academy
Conformations of Cyclohexanes III: Disubstituted
Conformations of Cyclohexanes IV: Trisubstituted

Videos
Cis- and trans-substituted cyclohexanes
cis- and trans-substituted cyclohexanes
3.3 Conformation of Cyclohexane is shared under a CC BY-NC-SA 4.0 license and was authored, remixed, and/or curated by LibreTexts.

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3.4 Chirality
Stereoisomers are isomers that differ in spatial arrangement of atoms, rather than order of atomic connectivity. One of their most
interesting type of isomer is the mirror-image stereoisomers, a non-superimposable set of two molecules that are mirror image of
one another. The existence of these molecules are determined by concept known as chirality.

Introduction
Organic compounds, molecules created around a chain of carbon atom (more commonly known as carbon backbone), play an
essential role in the chemistry of life. These molecules derive their importance from the energy they carry, mainly in a form of
potential energy between atomic molecules. Since such potential force can be widely affected due to changes in atomic placement,
it is important to understand the concept of an isomer, a molecule sharing same atomic make up as another but differing in
structural arrangements. This article will be devoted to a specific isomers called stereoisomers and its property of chirality (Figure
1).

Figure 1: Two enantiomers of a tetrahedral complex.

The concepts of steroisomerism and chirality command great deal of importance in modern organic chemistry, as these ideas helps
to understand the physical and theoretical reasons behind the formation and structures of numerous organic molecules, the main
reason behind the energy embedded in these essential chemicals. In contrast to more well-known constitutional isomerism, which
develops isotopic compounds simply by different atomic connectivity, stereoisomerism generally maintains equal atomic
connections and orders of building blocks as well as having same numbers of atoms and types of elements.
What, then, makes stereoisomers so unique? To answer this question, the learner must be able to think and imagine in not just two-
dimensional images, but also three-dimensional space. This is due to the fact that stereoisomers are isomers because their atoms are
different from others in terms of spatial arrangement.

Spatial Arrangement
First and foremost, one must understand the concept of spatial arrangement in order to understand stereoisomerism and chirality.
Spatial arrangement of atoms concern how different atomic particles and molecules are situated about in the space around the
organic compound, namely its carbon chain. In this sense, spatial arrangement of an organic molecule are different another if an
atom is shifted in any three-dimensional direction by even one degree. This opens up a very broad possibility of different
molecules, each with their unique placement of atoms in three-dimensional space .

Stereoisomers
Stereoisomers are, as mentioned above, contain different types of isomers within itself, each with distinct characteristics that
further separate each other as different chemical entities having different properties. Type called entaniomer are the previously-
mentioned mirror-image stereoisomers, and will be explained in detail in this article. Another type, diastereomer, has different
properties and will be introduced afterwards.

Enantiomers
This type of stereoisomer is the essential mirror-image, non-superimposable type of stereoisomer introduced in the beginning of the
article. Figure 3 provides a perfect example; note that the gray plane in the middle demotes the mirror plane.

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 Figure 2: Comparison of Chiral and Achiral Molecules. (a) Bromochlorofluoromethane is a chiral molecule whose stereocenter is
designated with an asterisk. Rotation of its mirror image does not generate the original structure. To superimpose the mirror
images, bonds must be broken and reformed. (b) In contrast, dichlorofluoromethane and its mirror image can be rotated so they are
superimposable.
Note that even if one were to flip over the left molecule over to the right, the atomic spatial arrangement will not be equal. This is
equivalent to the left hand - right hand relationship, and is aptly referred to as 'handedness' in molecules. This can be somewhat
counter-intuitive, so this article recommends the reader try the 'hand' example. Place both palm facing up, and hands next to each
other. Now flip either side over to the other. One hand should be showing the back of the hand, while the other one is showing the
palm. They are not same and non-superimposable.
This is where the concept of chirality comes in as one of the most essential and defining idea of stereoisomerism.

Chirality
Chirality essentially means 'mirror-image, non-superimposable molecules', and to say that a molecule is chiral is to say that its
mirror image (it must have one) is not the same as it self. Whether a molecule is chiral or achiral depends upon a certain set of
overlapping conditions. Figure 4 shows an example of two molecules, chiral and achiral, respectively. Notice the distinct
characteristic of the achiral molecule: it possesses two atoms of same element. In theory and reality, if one were to create a plane
that runs through the other two atoms, they will be able to create what is known as bisecting plane: The images on either side of the
plan is the same as the other (Figure 4).

Figure 4.
In this case, the molecule is considered 'achiral'. In other words, to distinguish chiral molecule from an achiral molecule, one must
search for the existence of the bisecting plane in a molecule. All chiral molecules are deprive of bisecting plane, whether simple or
complex.
As a universal rule, no molecule with different surrounding atoms are achiral. Chirality is a simple but essential idea to support the
concept of stereoisomerism, being used to explain one type of its kind. The chemical properties of the chiral molecule differs from
its mirror image, and in this lies the significance of chilarity in relation to modern organic chemistry.

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Compounds with Multiple Chiral Centers
We turn our attention next to molecules which have more than one stereocenter. We will start with a common four-carbon sugar
called D-erythrose.

A note on sugar nomenclature: biochemists use a special system to refer to the stereochemistry of sugar molecules, employing
names of historical origin in addition to the designators 'D' and 'L'. You will learn about this system if you take a biochemistry
class. We will use the D/L designations here to refer to different sugars, but we won't worry about learning the system.
As you can see, D-erythrose is a chiral molecule: C2 and C3 are stereocenters, both of which have the R configuration. In addition,
you should make a model to convince yourself that it is impossible to find a plane of symmetry through the molecule, regardless of
the conformation. Does D-erythrose have an enantiomer? Of course it does – if it is a chiral molecule, it must. The enantiomer of
erythrose is its mirror image, and is named L-erythrose (once again, you should use models to convince yourself that these mirror
images of erythrose are not superimposable).

Notice that both chiral centers in L-erythrose both have the S configuration. In a pair of enantiomers, all of the chiral centers are of
the opposite configuration.
What happens if we draw a stereoisomer of erythrose in which the configuration is S at C2 and R at C3? This stereoisomer, which is
a sugar called D-threose, is not a mirror image of erythrose. D-threose is a diastereomer of both D-erythrose and L-erythrose.

The definition of diastereomers is simple: if two molecules are stereoisomers (same molecular formula, same connectivity, different
arrangement of atoms in space) but are not enantiomers, then they are diastereomers by default. In practical terms, this means that
at least one - but not all - of the chiral centers are opposite in a pair of diastereomers. By definition, two molecules that are
diastereomers are not mirror images of each other.
L-threose, the enantiomer of D-threose, has the R configuration at C2 and the S configuration at C3. L-threose is a diastereomer of
both erythrose enantiomers.
In general, a structure with n stereocenters will have 2n different stereoisomers. (We are not considering, for the time being, the
stereochemistry of double bonds – that will come later). For example, let's consider the glucose molecule in its open-chain form
(recall that many sugar molecules can exist in either an open-chain or a cyclic form). There are two enantiomers of glucose, called

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D-glucose and L-glucose. The D-enantiomer is the common sugar that our bodies use for energy. It has n = 4 stereocenters, so
therefore there are 2n = 24 = 16 possible stereoisomers (including D-glucose itself).

In L-glucose, all of the stereocenters are inverted relative to D-glucose. That leaves 14 diastereomers of D-glucose: these are
molecules in which at least one, but not all, of the stereocenters are inverted relative to D-glucose. One of these 14 diastereomers, a
sugar called D-galactose, is shown above: in D-galactose, one of four stereocenters is inverted relative to D-glucose. Diastereomers
which differ in only one stereocenter (out of two or more) are called epimers. D-glucose and D-galactose can therefore be refered
to as epimers as well as diastereomers.

 Example 3.10

Draw the structure of L-galactose, the enantiomer of D-galactose.

Solution

 Example 3.11

Draw the structure of two more diastereomers of D-glucose. One should be an epimer.
Solution

Erythronolide B, a precursor to the 'macrocyclic' antibiotic erythromycin, has 10 stereocenters. It’s enantiomer is that molecule in
which all 10 stereocenters are inverted.

In total, there are 210 = 1024 stereoisomers in the erythronolide B family: 1022 of these are diastereomers of the structure above,
one is the enantiomer of the structure above, and the last is the structure above.
We know that enantiomers have identical physical properties and equal but opposite degrees of specific rotation. Diastereomers, in
theory at least, have different physical properties – we stipulate ‘in theory’ because sometimes the physical properties of two or
more diastereomers are so similar that it is very difficult to separate them. In addition, the specific rotations of diastereomers are
unrelated – they could be the same sign or opposite signs, and similar in magnitude or very dissimilar.

Constitutional isomers
Constitutational isomers or structural isomers are molecules with the same chemical formula but different structures of atoms
and bonds. For example, both 3-methylpentane and hexane have the same chemical formula, C6H14, yet they clearly have different

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structures:

3-methylpentane hexane

Another example involves functional groups. Methoxy methane, an ether, and ethanol, an alcohol, both have the chemical formula
C2H6O:

Methoxy methane Ethanol

External Resources
1. Further Details of Stereochemistry: For those interested in the topic further!
2. MIT Online-Lecture including basic Organic Chemistry : Good background lecture to introduce Organic Chemistry.
3. Chirality Rap: Good way to understand the concept? Decide for yourself!

References
1. Anslyn, Eric V. and Dougherty, Dennis A. Modern Physical Organic Chemistry. Chicago, IL.: University Science. 2005
2. Hick, Janice M. The Physical Chemistry of Chirality. New York, N.Y.: An American Chemical Society Publication. 2001.
3. Vollhardt, K. Peter C. and Schore, Neil E. Organic Chemistry: Structure and Function. Fifth Edition. New York, N.Y.: W. H.
Freeman Company, 2007.

Problems
Identify the following as either a constitutional isomer or stereoisomer. If stereoisomer, determine if it is an enantiomer or
diastereomer. Explain the reason behind the answer. Also mark chirality for each molecule.

1. 2. 3.

Contributors
Dan Chong
Jonathan Mooney (McGill University)

Further Reading on Chirality

Khan Academy
Introduction to Chirality

Cliffs Notes
Chirality

Web Pages

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Great Discussion of Chirality

Other Resources
Fun Chirality Game

Practice Problems
Principles of Chirality Problems
3.4 Chirality is shared under a CC BY-NC-SA 4.0 license and was authored, remixed, and/or curated by LibreTexts.
Chirality and Stereoisomers is licensed CC BY-NC-SA 4.0.

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3.5 Enantiomers
An atom with four groups attached to it can also adopt a tetrahedral geometry. This geometry often occurs when the central atom is
a little smaller. A tetrahedral geometry allows neighbouring groups to get a little farther from each other.
Unlike square planar compounds, simple tetrahedral compounds do not have the same kind of cis- and trans- isomers. That is, two
groups can't be placed on a tetrahedron so that they are opposite each other or beside each other. The relationship between any two
groups on a tetrahedron is the same as the relationship between any other two groups on a tetrahedron.
Dichlorodimethylsilane is a compound that can be used to make silicone polymers. Like platin, it has two each of two groups
attached to the central atom. However, the central tom is tetrahedral. There is only one way to arrange these four groups.

Figure SC3.1. A tetrahedral atom with two different types of groups attached, (CH3)2SiCl2.
However, if four different groups are attached to a tetrahedral atom, the four groups can be arranged in two possible ways. The two
compounds that result are mirror images of each other. These two isomers are called enantiomers.

Figure SC3.2. A pair of enantiomers. The (-) enantiomer is on the left and the (+) enantiomer is on the right. Note that the
tetrahedral silicon atom has four different groups attached.
Enantiomers are pairs of compounds with exactly the same connectivity but opposite three-dimensional shapes.
Enantiomers are not the same as each other; one enantiomer cannot be superimposed on the other.
Enantiomers are mirror images of each other.
Two compounds with the exact same connectivity, that are mirror images of each other but that are not identical to each other are
called enantiomers. The more common definition of an enantiomer is that it is not superimposable on its mirror image. It can be
distinguished easily from its mirror image, just as a right hand can easily be identified and distinguished from a left hand.
Compounds that occur in these pairs are called "chiral".
"Chiral" comes from the Greek word for "hand".
It can be shown using group theory, the mathematics of symmetry, that an enantiomer may also be defined as a molecule that does
not contain a mirror plane, meaning it cannot be divided into two identical and opposite halves.
Enantiomers contain no mirror planes.
Enantiomers do not contain two equal and opposite halves.
Unlike cis- and trans-isomers, two enantiomers have the same physical properties. they have the same melting point, the same
solubility, and so on. Two compounds that are almost identical, but mirror images of each other, have exactly the same kinds of
intermolecular attraction, so it may not be a surprise that their physical properties are identical.
Enantiomers are another example of a type of stereoisomers.
Two enantiomers have identical physical properties, except for optical rotation.
Optical rotation involves the interaction of plane-polarized light with a material. If a material is not symmetric, the light that passes
through it will be rotated. That means if the waves making up the light are oscillating in one direction as they enter the material,
they will have tilted slightly to oscillate in another direction when they emerge from the material. We will look at this phenomenon
later.
Two enantiomers have an equal but opposite rotational effect on plane-polarized light.
(+) enantiomers rotate light in a clockwise direction.
(-) enantiomers rotate light in a counterclockwise direction.
For example, in the chiral silicon compound shown above, the (+) enantiomer rotates plane-polarized light in a clockwise direction.
It has a "standard optical rotation" of [a] = +12 (+/-2)o. The (-) enantiomer rotates plane-polarized light in a counterclockwise

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direction. It has a "standard optical rotation" of [a] = -9.9 (+/-2)o.

Problem SC3.1.
A certain compound exists in two forms; enantiomer A and enantiomer B. Enantiomer A has a molecular weight of 126 g/mol, a
density of 0.995 g/mL, an optical rotation of [a] = 26o, a melting point of 65 oC, a boiling point of 225 oC, and an odour of citrus
fruit. What can you say about the corresponding properties of enantiomer B?

Contributors
Chris P Schaller, Ph.D., (College of Saint Benedict / Saint John's University)

Further Reading on Enantiomers

MasterOrganicChemistry
On Cats: Enantiocats

Carey 4th Edition On-Line Activity

What do I need to Know about Enantiomers?

Khan Academy
Chiral Examples 1

Chiral Examples 2

Cliffs Notes
Enantiomers and Diastereomers

Videos
Stereoisomers (Enantiomers) Video

Tutorial
Drawing Stereoisomers
3.5 Enantiomers is shared under a CC BY-NC-SA 4.0 license and was authored, remixed, and/or curated by LibreTexts.
Enantiomers by Chris Schaller is licensed CC BY-NC 3.0.

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3.6 Cahn-Ingold Prelog Rules
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 is also often called the Cahn-Ingold-Prelog rules. In addition to the Cahn-Ingold system, there are two ways of
experimentally determining the absolute configuration of an enantiomer:
1. X-ray diffraction analysis. Note that there is no correlation between the sign of rotation and the structure of a particular
enantiomer.
2. Chemical correlation with a molecule whose structure has already been determined via X-ray diffraction.
However, for non-laboratory purposes, it is beneficial to focus on the R/S system. The sign of optical rotation, although different
for the two enantiomers of a chiral molecule, at the same temperature, cannot be used to establish the absolute configuration of an
enantiomer; this is because the sign of optical rotation for a particular enantiomer may change when the temperature changes.

Stereocenters are labeled R or S

The "right hand" and "left hand" nomenclature is used to name the enantiomers of a chiral compound. The stereocenters are labeled
as R or S.

Consider the first picture: a curved arrow is drawn from the highest priority (1) substituent to the lowest priority (4) substituent. If
the arrow points in a counterclockwise direction (left when leaving the 12 o' clock position), the configuration at stereocenter is
considered S ("Sinister" → Latin= "left"). If, however, the arrow points clockwise,(Right when leaving the 12 o' clock position)
then the stereocenter is labeled R ("Rectus" → Latin= "right"). The R or S is then added as a prefix, in parenthesis, to the name of
the enantiomer of interest. For example: (R)-2-Bromobutane and (S)-2,3- Dihydroxypropanal.

Sequence rules to assign priorities to substituents

Before applying the R and S nomenclature to a stereocenter, the substituents must be prioritized according to the following rules:

Rule 1
First, examine at the atoms directly attached to the stereocenter of the compound. A substituent with a higher atomic number takes
precedence over a substituent with a lower atomic number. Hydrogen is the lowest possible priority substituent, because it has the
lowest atomic number.
1. When dealing with isotopes, the atom with the higher atomic mass receives higher priority.
2. When visualizing the molecule, the lowest priority substituent should always point away from the viewer (a dashed line
indicates this). To understand how this works or looks, imagine that a clock and a pole. Attach the pole to the back of the clock,
so that when when looking at the face of the clock the pole points away from the viewer in the same way the lowest priority
substituent should point away.
3. Then, draw an arrow from the highest priority atom to the 2nd highest priority atom to the 3rd highest priority atom. Because
the 4th highest priority atom is placed in the back, the arrow should appear like it is going across the face of a clock. If it is
going clockwise, then it is an R-enantiomer; If it is going counterclockwise, it is an S-enantiomer.
When looking at a problem with wedges and dashes, if the lowest priority atom is not on the dashed line pointing away, the
molecule must be rotated.
Remember that

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 Wedges indicate coming towards the viewer.
Dashes indicate pointing away from the viewer.

Rule 2
If there are two substituents with equal rank, proceed along the two substituent chains until there is a point of difference. First,
determine which of the chains has the first connection to an atom with the highest priority (the highest atomic number). That chain
has the higher priority.
If the chains are similar, proceed down the chain, until a point of difference.
For example: an ethyl substituent takes priority over a methyl substituent. At the connectivity of the stereocenter, both have a
carbon atom, which are equal in rank. Going down the chains, a methyl has only has hydrogen atoms attached to it, whereas the
ethyl has another carbon atom. The carbon atom on the ethyl is the first point of difference and has a higher atomic number than
hydrogen; therefore the ethyl takes priority over the methyl.

Rule 3
If a chain is connected to the same kind of atom twice or three times, check to see if the atom it is connected to has a greater atomic
number than any of the atoms that the competing chain is connected to.
If none of the atoms connected to the competing chain(s) at the same point has a greater atomic number: the chain bonded to the
same atom multiple times has the greater priority
If however, one of the atoms connected to the competing chain has a higher atomic number: that chain has the higher priority.

 Example 2

A 1-methylethyl substituent takes precedence over an ethyl substituent. Connected to the first carbon atom, ethyl only has one
other carbon, whereas the 1-methylethyl has two carbon atoms attached to the first; this is the first point of difference.
Therefore, 1-methylethyl ranks higher in priority than ethyl, as shown below:

However:

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 Remember that being double or triple bonded to an atom means that the atom is connected to the same atom twice. In such a
case, follow the same method as above.

Caution!!
Keep in mind that priority is determined by the first point of difference along the two similar substituent chains. After the first
point of difference, the rest of the chain is irrelevant.

When looking for the first point of difference on similar substituent chains, one may encounter branching. If there is branching,
choose the branch that is higher in priority. If the two substituents have similar branches, rank the elements within the branches
until a point of difference.

After all your substituents have been prioritized in the correct manner, you can now name/label the molecule R or S.
1. Put the lowest priority substituent in the back (dashed line).
2. Proceed from 1 to 2 to 3. (it is helpful to draw or imagine an arcing arrow that goes from 1--> 2-->3)
3. Determine if the direction from 1 to 2 to 3 clockwise or counterclockwise.
i) If it is clockwise it is R.
ii) if it is counterclockwise it is S.

USE YOUR MODELING KIT: Models assist in visualizing the structure. When using a model, make sure the lowest priority is
pointing away from you. Then determine the direction from the highest priority substituent to the lowest: clockwise (R) or
counterclockwise (S).

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IF YOU DO NOT HAVE A MODELING KIT: remember that the dashes mean the bond is going into the screen and the wedges
means that bond is coming out of the screen. If the lowest priority bond is not pointing to the back, mentally rotate it so that it is.
However, it is very useful when learning organic chemistry to use models.
If you have a modeling kit use it to help you solve the following practice problems.

 Exercise 1

Are the following R or S?

Answer
1. S: I > Br > F > H. The lowest priority substituent, H, is already going towards the back. It turns left going from I to Br
to F, so it's a S.
2. R: Br > Cl > CH3 > H. You have to switch the H and Br in order to place the H, the lowest priority, in the back. Then,
going from Br to Cl, CH3 is turning to the right, giving you a R.
3. Neither R or S: This molecule is achiral. Only chiral molecules can be named R or S.
4. R: OH > CN > CH2NH2 > H. The H, the lowest priority, has to be switched to the back. Then, going from OH to CN to
CH2NH2, you are turning right, giving you a R. (5)
5. S: −COOH > −CH OH > C≡CH > H. Then, going from −COOH to −CH OH to −C≡CH you are turning left,
2 2

giving you a S configuration.

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.

Further Reading

MasterOrganicChemistry
The Single Swap Rule

The R-S Toggle

Carey 4th Edition On-Line Activity

How to Name Enantiomers?

Khan Academy

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Cahn-Ingold-Prelog System for Naming Enantiomers

R,S(Cahn-Ingold-Prelog) Naming System Example 2

R,S System for Determining Absolute Configuration

R,S System for Cyclic Compounds

Cliffs Notes
Cahn-Ingold-Prelog RS Notation System

Web Pages
R and S Isomers
Priority Rules
R and S Naming
Naming Enantiomers
R and S Naming Conventions
CHM 25500 Handout on R and S

Videos
Freelance Teacher R and S Naming
Naming Enantiomers

Tutorial
Assigning Chiral Centers
3D Molecules

Other Resources
JAVA App on Assigning Priorities
3.6 Cahn-Ingold Prelog Rules is shared under a CC BY-NC-SA 4.0 license and was authored, remixed, and/or curated by LibreTexts.
Absolute Configuration - R-S Sequence Rules by Ekta Patel, Ifemayowa Aworanti is licensed CC BY-NC-SA 4.0.

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3.7 Diastereomers
Diastereomers are stereoisomers that are not related as object and mirror image and are not enantiomers. Unlike enatiomers which
are mirror images of each other and non-sumperimposable, diastereomers are not mirror images of each other and non-
superimposable. Diastereomers can have different physical properties and reactivity. They have different melting points and
boiling points and different densities. They have two or more stereocenters.

Introduction
It is easy to mistake between diasteromers and enantiomers. For example, we have four steroisomers of 3-bromo-2-butanol. The
four possible combination are SS, RR, SR and RS (Figure 1). One of the molecule is the enantiomer of its mirror image molecule
and diasteromer of each of the other two molecule (SS is enantiomer of RR and diasteromer of RS and SR). SS's mirror image is
RR and they are not superimposable, so they are enantiomers. RS and SR are not mirror image of SS and are not superimposable to
each other, so they are diasteromers.

Figure 1

Diastereomers vs. Enantiomers vs. Meso Compounds

Tartaric acid, C4H6O6, is an organic compound that can be found in grape, bananas, and in wine. The structures of tartaric acid
itself is really interesting. Naturally, it is in the form of (R,R) stereocenters. Artificially, it can be in the meso form (R,S), which is
achiral. R,R tartaric acid is enantiomer to is mirror image which is S,S tartaric acid and diasteromers to meso-tartaric acid (figure
2).
(R,R) and (S,S) tartaric acid have similar physical properties and reactivity. However, meso-tartaric acid have different physical
properties and reactivity. For example, melting point of (R,R) & (S,S) tartaric is about 170 degree Celsius, and melting point of
meso-tartaric acid is about 145 degree Celsius.

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 Figure 2
To identify meso, meso compound is superimposed on its mirror image, and has an internal plane that is symmetry (figure 3).
Meso-tartaric acid is achiral and optically unactive.

Problems
Identify which of the following pair is enantiomers, diastereomers or meso compounds.

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Answer
a. Diasteromers
b. Identical
c. Meso
d. Enantiomers

Outside Links
http://www.sparknotes.com/chemistry/...section2.rhtml
http://en.Wikipedia.org/wiki/Diastereomer
http://en.Wikipedia.org/wiki/Tartaric_acid

Further Reading on Diastereomers

MasterOrganicChemistry
On Cats: Enantiocats vs. Diastereocats

Khan Academy
Diastereomers

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Cliffs Notes
Enantiomers and Diastereomers

Web Pages
WikiBooks Diastereomers

Diastereomer Definition

Sparknotes Diastereomers
3.7 Diastereomers is shared under a CC BY-NC-SA 4.0 license and was authored, remixed, and/or curated by LibreTexts.
Diastereomers is licensed CC BY-NC-SA 4.0.

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3.8 Meso Isomers
Meso compounds are achiral compounds that has multiple chiral centers. It is superimposed on its mirror image and is optically
inactive despite its stereocenters.

Introduction
In general, a meso compound should contain two or more identical substituted stereocenters. Also, it has an internal symmetry
plane that divides the compound in half. These two halves reflect each other by the internal mirror. The stereochemistry of
stereocenters should "cancel out". What it means here is that when we have an internal plane that splits the compound into two
symmetrical sides, the stereochemistry of both left and right side should be opposite to each other, and therefore, result in optically
inactive. Cyclic compounds may also be meso.

Identification
If A is a meso compound, it should have two or more stereocenters, an internal plane, and the stereochemistry should be R and S.
1. Look for an internal plane, or internal mirror, that lies in between the compound.
2. The stereochemistry (e.g. R or S) is very crucial in determining whether it is a meso compound or not. As mentioned above, a
meso compound is optically inactive, so their stereochemistry should cancel out. For instance, R cancels S out in a meso
compound with two stereocenters.

trans-1,2-dichloro-1,2-ethanediol

(meso)-2,3-dibromobutane
Tips: An interesting thing about single bonds or sp3-orbitals is that we can rotate the substituted groups that attached to a
stereocenter around to recognize the internal plane. As the molecule is rotated, its stereochemistry does not change. For example:

Another case is when we rotate the whole molecule by 180 degree. Both molecules below are still meso.

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Remember the internal plane here is depicted on two dimensions. However, in reality, it is three dimensions, so be aware of it when
we identify the internal mirror.

 Example

This molecule has a plane of symmetry (the horizontal plane going through the red broken line) and, therefore, is achiral;
However, it has two chiral carbons and is consequentially a meso compound.

 Example 2

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 cyclobutane. They do not
necessarily have to be two stereocenters, but can have more.

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Optical Activity Analysis
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 (+).

Problems
Beside meso, there are also other types of molecules: enantiomer, diastereomer, and identical. Determine if the following molecules
are meso.

Answer key: A C, D, E are meso compounds.

References
1. Vollhardt, K. P.C. & Shore, N. (2007). Organic Chemistry (5thEd.). New York: W. H. Freeman. (190-192)
2. Shore, N. (2007). Study Guide and Solutions Manual for Organic Chemistry (5th Ed.). New York: W.H. Freeman. (70-80)

Contributors
Duy Dang
Gamini Gunawardena from the OChemPal site (Utah Valley University)

Further Reading

MasterOrganicChemistry
On Cats: Moe the Meso Cat
The Meso Trap

Khan Academy

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Meso Compounds
3.8 Meso Isomers is shared under a CC BY-NC-SA 4.0 license and was authored, remixed, and/or curated by LibreTexts.
Meso Compounds is licensed CC BY-NC-SA 4.0.

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3.9 Cis/Trans Isomerism
Geometric Isomerism of Alkenes
Geometric isomerism (also known as cis-trans isomerism or E-Z isomerism) is a form of stereoisomerism. This page explains what
stereoisomers are and how you recognise the possibility of geometric isomers in a molecule.

What are isomers?

Isomers are molecules that have the same molecular formula, but have a different arrangement of the atoms in space. That excludes
any different arrangements which are simply due to the molecule rotating as a whole, or rotating about particular bonds. Where the
atoms making up the various isomers are joined up in a different order, this is known as structural isomerism. Structural isomerism
is not a form of stereoisomerism, and is dealt with on a separate page.
In stereoisomerism, the atoms making up the isomers are joined up in the same order, but still manage to have a different spatial
arrangement. Geometric isomerism is one form of stereoisomerism.

Geometric (cis / trans) isomerism

These isomers occur where you have restricted rotation somewhere in a molecule. At an introductory level in organic chemistry,
examples usually just involve the carbon-carbon double bond - and that's what this page will concentrate on. Think about what
happens in molecules where there is unrestricted rotation about carbon bonds - in other words where the carbon-carbon bonds are
all single. The next diagram shows two possible configurations of 1,2-dichloroethane.

These two models represent exactly the same molecule. You can get from one to the other just by twisting around the carbon-
carbon single bond. These molecules are not isomers.
If you draw a structural formula instead of using models, you have to bear in mind the possibility of this free rotation about single
bonds. You must accept that these two structures represent the same molecule:

But what happens if you have a carbon-carbon double bond - as in 1,2-dichloroethene?

These two molecules are not the same. The carbon-carbon double bond won't rotate and so you would have to take the models to
pieces in order to convert one structure into the other one. That is a simple test for isomers. If you have to take a model to pieces to
convert it into another one, then you've got isomers. If you merely have to twist it a bit, then you haven't!
Drawing structural formulae for the last pair of models gives two possible isomers:
1. In one, the two chlorine atoms are locked on opposite sides of the double bond. This is known as the trans isomer. (trans : from
latin meaning "across" - as in transatlantic).
2. In the other, the two chlorine atoms are locked on the same side of the double bond. This is know as the cis isomer. (cis : from
latin meaning "on this side")

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The most likely example of geometric isomerism you will meet at an introductory level is but-2-ene. In one case, the CH3 groups
are on opposite sides of the double bond, and in the other case they are on the same side.

The importance of drawing geometric isomers properly

It's very easy to miss geometric isomers in exams if you take short-cuts in drawing the structural formulae. For example, it is very
tempting to draw but-2-ene as
CH3CH=CHCH3
If you write it like this, you will almost certainly miss the fact that there are geometric isomers. If there is even the slightest hint in
a question that isomers might be involved, always draw compounds containing carbon-carbon double bonds showing the correct
bond angles (120°) around the carbon atoms at the ends of the bond. In other words, use the format shown in the last diagrams
above.

How to recognize the possibility of geometric isomerism

You obviously need to have restricted rotation somewhere in the molecule. Compounds containing a carbon-carbon double bond
have this restricted rotation. (Other sorts of compounds may have restricted rotation as well, but we are concentrating on the case
you are most likely to meet when you first come across geometric isomers.) If you have a carbon-carbon double bond, you need to
think carefully about the possibility of geometric isomers.
What needs to be attached to the carbon-carbon double bond?
Think about this case:

Although we've swapped the right-hand groups around, these are still the same molecule. To get from one to the other, all you
would have to do is to turn the whole model over. You won't have geometric isomers if there are two groups the same on one end of
the bond - in this case, the two pink groups on the left-hand end. So there must be two different groups on the left-hand carbon and
two different groups on the right-hand one. The cases we've been exploring earlier are like this:

But you could make things even more different and still have geometric isomers:

Here, the blue and green groups are either on the same side of the bond or the opposite side. Or you could go the whole hog and
make everything different. You still get geometric isomers, but by now the words cis and trans are meaningless. This is where the
more sophisticated E-Z notation comes in.

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Summary
To get geometric isomers you must have:
restricted rotation (often involving a carbon-carbon double bond for introductory purposes);
two different groups on the left-hand end of the bond and two different groups on the right-hand end. It doesn't matter whether
the left-hand groups are the same as the right-hand ones or not.

Contributors
Jim Clark (Chemguide.co.uk)

Cis/Trans Isomerism in Rings

Rings: cis/trans and axial/equatorial relationships

Further Reading

Khan Academy
cis/trans and E/Z naming for alkenes

Wikipedia
Cis/trans isomerism

Video
How to draw cis and trans isomers
3.9 Cis/Trans Isomerism is shared under a CC BY-NC-SA 4.0 license and was authored, remixed, and/or curated by LibreTexts.
Geometric Isomerism in Organic Molecules by Jim Clark is licensed CC BY-NC 4.0.

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 CHAPTER OVERVIEW

Chapter 4. Intermolecular Forces and Physical Properties

Purdue CHM 26505: Organic

Chemistry for Chemistry Majors (1st
Semester)
Fall 2014: Prof. Mark Lipton

Template:HideTOC

Topic hierarchy
4.1 Bond Polarity and Molecular Dipoles
4.2 Intermolecular Forces
4.3 Boiling Points
4.4 Solubility
4.5 Chromatography

Chapter 4. Intermolecular Forces and Physical Properties is shared under a CC BY-NC-SA 4.0 license and was authored, remixed, and/or curated by
LibreTexts.

1
4.1 Bond Polarity and Molecular Dipoles
Dipole moments occur when there is a separation of charge. They can occur between two ions in an ionic bond or between atoms in
a covalent bond; dipole moments arise from differences in electronegativity. The larger the difference in electronegativity, the
larger the dipole moment. The distance between the charge separation is also a deciding factor in the size of the dipole moment.
The dipole moment is a measure of the polarity of the molecule.

Introduction
When atoms in a molecule share electrons unequally, they create what is called a dipole moment. This occurs when one atom is
more electronegative than another, resulting in that atom pulling more tightly on the shared pair of electrons, or when one atom has
a lone pair of electrons and the difference of electronegativity vector points in the same way. One of the most common examples is
the water molecule, made up of one oxygen atom and two hydrogen atoms. The differences in electronegativity and lone electrons
give oxygen a partial negative charge and each hydrogen a partial positive charge.

Dipole Moment
When two electrical charges, of opposite sign and equal magnitude, are separated by a distance, an electric dipole is established.
The size of a dipole is measured by its dipole moment (μ ). Dipole moment is measured in Debye units, which is equal to the
distance between the charges multiplied by the charge (1 Debye equals 3.34 × 10 C m ). The dipole moment of a molecule can
−30

be calculated by Equation 1:

μ⃗ = ∑ qi r i⃗ (1)

where
μ⃗ is the dipole moment vector
qi is the magnitude of the i charge, and
th

r i⃗ is the vector representing the position of i

th
charge.
The dipole moment acts in the direction of the vector quantity. An example of a polar molecule is H O . Because of the lone pair on
2

oxygen, the structure of H O is bent (via VSEPR theory), which means that the vectors representing the dipole moment of each
2

bond do not cancel each other out. Hence, water is polar.

Figure 1: Dipole moment of water. The convention in chemistry is that the arrow representing the dipole moment goes from
positive to negative. Physicist tend to use the opposite orientation.
The vector points from positive to negative, on both the molecular (net) dipole moment and the individual bond dipoles. Table A2
shows the electronegativity of some of the common elements. The larger the difference in electronegativity between the two atoms,
the more electronegative that bond is. To be considered a polar bond, the difference in electronegativity must be large. The dipole
moment points in the direction of the vector quantity of each of the bond electronegativities added together.
It is relatively easy to measure dipole moments: just place a substance between charged plates (Figure 2); polar molecules increase
the charge stored on the plates, and the dipole moment can be obtained (i.e., via the capacitance of the system). Nonpolar CCl is 4

not deflected; moderately polar acetone deflects slightly; highly polar water deflects strongly. In general, polar molecules will align
themselves: (1) in an electric field, (2) with respect to one another, or (3) with respect to ions (Figure 2).

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 Figure 2: Polar molecules align themselves in an electric field (left), with respect to one another (middle), and with respect to ions
(right)
Equation 1 can be simplified for a simple separated two-charge system like diatomic molecules or when considering a bond dipole
within a molecule
μdiatomic = Q × r (2)

This bond dipole 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. Consider a simple system of a
+ −

single electron and proton separated by a fixed distance. When the proton and electron are close together, the dipole moment
(degree of polarity) decreases. However, as the proton and electron get farther apart, the dipole moment increases. In this case, the
dipole moment is calculated as (via Equation 2):
μ = Qr

−19 −10
= (1.60 × 10 C )(1.00 × 10 m)

−29
= 1.60 × 10 C ⋅m

The Debye characterizes the size of the dipole moment. When a proton and electron are 100 pm apart, the dipole moment is
4.80 D:

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

= 4.80 D

4.80 D is a key reference value and represents a pure charge of +1 and -1 separated by 100 pm. If the charge separation is
increased then the dipole moment increases (linearly):
If the proton and electron are separated by 120 pm:
120
μ = (4.80 D) = 5.76 D (3)
100

If the proton and electron are separated by 150 pm:

150
μ = (4.80 D) = 7.20 D (4)
100

If the proton and electron are separated by 200 pm:

200
μ = (4.80 D) = 9.60 D (5)
100

 Example 1 : Water

The water molecule in Figure 1 can be used to determine the direction and magnitude of the dipole moment. From the
electronegativities of oxygen and hydrogen, the difference in electronegativity 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 the O-H bond =1.5 D, so the net dipole moment is

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 104.5˚
μ = 2(1.5) cos( ) = 1.84 D
2

Polarity and Structure of Molecules

The shape of a molecule and the polarity of its bonds determine the OVERALL POLARITY of that molecule. A molecule that
contains polar bonds might not have any overall polarity, depending upon its shape. The simple definition of whether a complex
molecule is polar or not depends upon whether its overall centers of positive and negative charges overlap. If these centers lie at the
same point in space, then the molecule has no overall polarity (and is non polar). If a molecule is completely symmetric, then the
dipole moment vectors on each molecule will cancel each other out, making the molecule nonpolar. A molecule can only be polar if
the structure of that molecule is not symmetric.

Figure 3: Charge distributions of CO and H

2 2
O \). Blue and red colored regions are negatively and positively signed regions,
respectively. (CC BY-SA-NC 3.0; anonymous)
A good example of a nonpolar molecule that contains polar bonds is carbon dioxide (Figure 3a). This is a linear molecule and each
C=O bond is, in fact, polar. The central carbon will have a net positive charge, and the two outer oxygen atoms a net negative
charge. However, since the molecule is linear, these two bond dipoles cancel each other out (i.e. the vector addition of the dipoles
equals zero) and the overall molecule has a zero dipole moment (μ = 0 ).

Although a polar bond is a prerequisite for a molecule to have a dipole, not all molecules
with polar bonds exhibit dipoles
For AB molecules, where A is the central atom and B are all the same types of atoms, there are certain molecular geometries
n

which are symmetric. Therefore, they will have no dipole even if the bonds are polar. These geometries include linear, trigonal
planar, tetrahedral, octahedral and trigonal bipyramid.

Figure 4: Molecular geometries with exact cancellation of polar bonding to generate a non-polar molecule (μ = 0 )

 Example 3 : C 2
Cl
4

Although the C–Cl bonds are rather polar, the individual bond dipoles cancel one another in this symmetrical structure, and
Cl C=CCl does not have a net dipole moment.
2 2

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  Example 3 : CH 3
Cl

C-Cl, the key polar bond, is 178 pm. Measurement reveals 1.87 D. From this data, % ionic character can be computed. If this
bond were 100% ionic (based on proton & electron),
178
μ = (4.80 D)
100

= 8.54 D

Although the bond length is increasing, the dipole is decreasing as you move down the halogen group. The electronegativity
decreases as we move down the group. Thus, the greater influence is the electronegativity of the two atoms (which influences the
charge at the ends of the dipole).
Table 1: Relationship between Bond length, Electronegativity and Dipole moments in simple Diatomics
Compound Bond Length (Å) Electronegativity Difference Dipole Moment (D)

HF 0.92 1.9 1.82

HCl 1.27 0.9 1.08

HBr 1.41 0.7 0.82

HI 1.61 0.4 0.44

References
1. Housecroft, Catherine E. and Alan G. Sharpe. Inorganic Chemistry. 3rd ed. Harlow: Pearson Education, 2008. Print. (Pages
44-46)
2. Tro, Nivaldo J. Chemistry: A Molecular Approach. Upper Saddle River: Pearson Education, 2008. Print. (Pages 379-386)

Further Reading

MasterOrganicChemistry
Partial Charges
Web Pages
Electronegativity and Polar Bonds
Videos

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Identifying Polar Covalent Bonds in Organic Molecules
4.1 Bond Polarity and Molecular Dipoles is shared under a CC BY-NC-SA 4.0 license and was authored, remixed, and/or curated by LibreTexts.
Dipole Moments by Delmar Larsen, Mike Blaber is licensed CC BY 4.0.

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4.2 Intermolecular Forces
Skills to Develop
To describe the intermolecular forces in liquids.

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.

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 at high pressures. (For more
information on the behavior of real gases and deviations from the ideal gas law,.)
In this section, we explicitly consider three kinds of intermolecular 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. The first two are often described
collectively as van der Waals forces.

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 1a.

Figure 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.
These arrangements are more stable than arrangements in which two positive or two negative ends are adjacent (Figure 1c). Hence
dipole–dipole interactions, such as those in Figure 1b, are attractive intermolecular interactions, whereas those in Figure 1d are
repulsive intermolecular interactions. Because molecules in a liquid move freely and continuously, molecules always experience

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both attractive and repulsive dipole–dipole interactions simultaneously, as shown in Figure 2. On average, however, the attractive
interactions dominate.

Figure 2 : Both Attractive and Repulsive Dipole–Dipole Interactions Occur in a Liquid Sample with Many Molecules
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
much more rapidly with increasing distance than do the 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 interionic
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 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 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

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

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 Given: compounds
Asked for: order of increasing boiling points
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 electronegativities. 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.

Exercise 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 (Table 2).
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 : 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

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 Substance Molar Mass (g/mol) Melting Point (°C) Boiling Point (°C)

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 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.

Figure 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
3 , tends to become more pronounced as atomic and molecular masses increase (Table 2 ). 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

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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.

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 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 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).

Figure 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
Arrange n-butane, propane, 2-methylpropane [isobutene, (CH3)2CHCH3], and n-pentane in order of increasing boiling points.
Given: compounds
Asked for: 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).

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 Exercise 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 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
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 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 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

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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 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, cagelike 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.

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.

Example 3
Considering CH3OH, C2H6, Xe, and (CH3)3N, which can form hydrogen bonds with themselves? Draw the hydrogen-bonded
structures.
Given: compounds
Asked for: formation of hydrogen bonds and structure
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

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 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:

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

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 4 : Buckyballs
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

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

Additional Reading
Links to Different Intermolecular Forces
List of Intermolecular Forces

Further Reading on Intermolecular Forces

MasterOrganicChemistry
The Four Intermolecular Forces and How they Affect Boiling Points
Khan Academy
Intermolecular Forces in Organic Chemistry

Web Pages
Description of Intermolecular Forces
Intermolecular Forces Summary
Detailed Link on Intermolecular Forces
Hydrogen Bonding
van der Waals Forces

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Practice Problems
Virtual Text
4.2 Intermolecular Forces is shared under a CC BY-NC-SA 4.0 license and was authored, remixed, and/or curated by LibreTexts.

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4.3 Boiling Points
For general purposes it is useful to consider temperature to be a measure of the kinetic energy of all the atoms and molecules in a
given system. As temperature is increased, there is a corresponding increase in the vigor of translational and rotation motions of all
molecules, as well as the vibrations of atoms and groups of atoms within molecules. Experience shows that many compounds exist
normally as liquids and solids; and that even low-density gases, such as hydrogen and helium, can be liquified at sufficiently low
temperature and high pressure. A clear conclusion to be drawn from this fact is that intermolecular attractive forces vary
considerably, and that the boiling point of a compound is a measure of the strength of these forces. Thus, in order to break the
intermolecular attractions that hold the molecules of a compound in the condensed liquid state, it is necessary to increase their
kinetic energy by raising the sample temperature to the characteristic boiling point of the compound.
The following table illustrates some of the factors that influence the strength of intermolecular attractions. The formula of each
entry is followed by its formula weight in parentheses and the boiling point in degrees Celsius. First there is molecular size. Large
molecules have more electrons and nuclei that create van der Waals attractive forces, so their compounds usually have higher
boiling points than similar compounds made up of smaller molecules. It is very important to apply this rule only to like compounds.
The examples given in the first two rows are similar in that the molecules or atoms are spherical in shape and do not have
permanent dipoles. Molecular shape is also important, as the second group of compounds illustrate. The upper row consists of
roughly spherical molecules, whereas the isomers in the lower row have cylindrical or linear shaped molecules. The attractive
forces between the latter group are generally greater. Finally, permanent molecular dipoles generated by polar covalent bonds result
in even greater attractive forces between molecules, provided they have the mobility to line up in appropriate orientations. The last
entries in the table compare non-polar hydrocarbons with equal-sized compounds having polar bonds to oxygen and nitrogen.
Halogens also form polar bonds to carbon, but they also increase the molecular mass, making it difficult to distinguish among these
factors.
Table 1: Boiling Points (ºC) of Selected Elements and Compounds

Increasing Size

Atomic Ar (40) -186 Kr (83) -153 Xe (131) -109

Molecular CH4 (16) -161 (CH3)4C (72) 9.5 (CH3)4Si (88) 27 CCl4 (154) 77

Molecular Shape

Spherical: (CH3)4C (72) 9.5 (CH3)2CCl2 (113) 69 (CH3)3CC(CH3)3 (114) 106

Linear: CH3(CH2)3CH3 (72) 36 Cl(CH2)3Cl (113) 121 CH3(CH2)6CH3 (114) 126

Molecular Polarity

Non-polar: H2C=CH2 (28) -104 F2 (38) -188 CH3C≡CCH3 (54) -32 CF4 (88) -130

H2C=O (30) -21 CH3CH=O (44) 20 (CH3)3N (59) 3.5 (CH3)2C=O (58) 56
Polar:
HC≡N (27) 26 CH3C≡N (41) 82 (CH2)3O (58) 50 CH3NO2 (61) 101

The melting points of crystalline solids cannot be categorized in as simple a fashion as boiling points. The distance between
molecules in a crystal lattice is small and regular, with intermolecular forces serving to constrain the motion of the molecules more
severely than in the liquid state. Molecular size is important, but shape is also critical, since individual molecules need to fit
together cooperatively for the attractive lattice forces to be large. Spherically shaped molecules generally have relatively high
melting points, which in some cases approach the boiling point. This reflects the fact that spheres can pack together more closely
than other shapes. This structure or shape sensitivity is one of the reasons that melting points are widely used to identify specific
compounds. The data in the following table serves to illustrate these points.

Compound Formula Boiling Point Melting Point

pentane CH3(CH2)3CH3 36ºC –130ºC

hexane CH3(CH2)4CH3 69ºC –95ºC

heptane CH3(CH2)5CH3 98ºC –91ºC

octane CH3(CH2)6CH3 126ºC –57ºC

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 nonane CH3(CH2)7CH3 151ºC –54ºC

decane CH3(CH2)8CH3 174ºC –30ºC

tetramethylbutane (CH3)3C-C(CH3)3 106ºC +100ºC

Notice that the boiling points of the unbranched alkanes (pentane through decane) increase rather smoothly with molecular weight,
but the melting points of the even-carbon chains increase more than those of the odd-carbon chains. Even-membered chains pack
together in a uniform fashion more compactly than do odd-membered chains. The last compound, an isomer of octane, is nearly
spherical and has an exceptionally high melting point (only 6º below the boiling point).

Contributors
William Reusch, Professor Emeritus (Michigan State U.), Virtual Textbook of Organic Chemistry

Further Reading

MasterOrganicChemistry
3 Trends That Affect Boiling Points

Websites
Boiling Point Tutorial
Slide Show on Determining Boiling Points
4.3 Boiling Points is shared under a CC BY-NC-SA 4.0 license and was authored, remixed, and/or curated by LibreTexts.

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4.4 Solubility
An understanding of bond dipoles and the various types of noncovalent intermolecular forces allows us to explain, on a molecular
level, many observable physical properties of organic compounds. In this section, we will concentrate on solubility, melting point,
and boiling point.

Solubility
Virtually all of the organic chemistry that you will see in this course takes place in the solution phase. In the organic laboratory,
reactions are often run in nonpolar or slightly polar solvents such as toluene (methylbenzene), hexane, dichloromethane, or
diethylether. In recent years, much effort has been made to adapt reaction conditions to allow for the use of ‘greener’ (in other
words, more environmentally friendly) solvents such as water or ethanol, which are polar and capable of hydrogen bonding. In
organic reactions that occur in the cytosolic region of a cell, the solvent is of course water. It is critical for any organic chemist to
understand the factors which are involved in the solubility of different molecules in different solvents.
You probably remember the rule you learned in general chemistry regarding solubility: ‘like dissolves like’ (and even before you
took any chemistry at all, you probably observed at some point in your life that oil does not mix with water). Let’s revisit this old
rule, and put our knowledge of covalent and noncovalent bonding to work.
Imagine that you have a flask filled with water, and a selection of substances that you will test to see how well they dissolve in the
water. The first substance is table salt, or sodium chloride. As you would almost certainly predict, especially if you’ve ever
inadvertently taken a mouthful of water while swimming in the ocean, this ionic compound dissolves readily in water. Why?
Because water, as a very polar molecule, is able to form many ion-dipole interactions with both the sodium cation and the chloride
anion, the energy from which is more than enough to make up for energy required to break up the ion-ion interactions in the salt
crystal and some water-water hydrogen bonds.

The end result, then, is that in place of sodium chloride crystals, we have individual sodium cations and chloride anions surrounded
by water molecules – the salt is now in solution. Charged species as a rule dissolve readily in water: in other words, they are very
hydrophilic (water-loving).
Now, we’ll try a compound called biphenyl, which, like sodium chloride, is a colorless crystalline substance (the two compounds
are readily distinguishable by sight, however – the crystals look quite different).

Biphenyl does not dissolve at all in water. Why is this? Because it is a very non-polar molecule, with only carbon-carbon and
carbon-hydrogen bonds. It is able to bond to itself very well through nonpolar van der Waals interactions, but it is not able to form
significant attractive interactions with the very polar solvent molecules. Thus, the energetic cost of breaking up the biphenyl-to-
biphenyl interactions in the solid is high, and very little is gained in terms of new biphenyl-water interactions. Water is a terrible
solvent for nonpolar hydrocarbon molecules: they are very hydrophobic (water-hating).
Next, you try a series of increasingly large alcohol compounds, starting with methanol (1 carbon) and ending with octanol (8
carbons).

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You find that the smaller alcohols - methanol, ethanol, and propanol - dissolve easily in water. This is because the water is able to
form hydrogen bonds with the hydroxyl group in these molecules, and the combined energy of formation of these water-alcohol
hydrogen bonds is more than enough to make up for the energy that is lost when the alcohol-alcohol hydrogen bonds are broken up.
When you try butanol, however, you begin to notice that, as you add more and more to the water, it starts to form its own layer on
top of the water.
The longer-chain alcohols - pentanol, hexanol, heptanol, and octanol - are increasingly non-soluble. What is happening here?
Clearly, the same favorable water-alcohol hydrogen bonds are still possible with these larger alcohols. The difference, of course, is
that the larger alcohols have larger nonpolar, hydrophobic regions in addition to their hydrophilic hydroxyl group. At about four or
five carbons, the hydrophobic effect begins to overcome the hydrophilic effect, and water solubility is lost.
Now, try dissolving glucose in the water – even though it has six carbons just like hexanol, it also has five hydrogen-bonding,
hydrophilic hydroxyl groups in addition to a sixth oxygen that is capable of being a hydrogen bond acceptor.

We have tipped the scales to the hydrophilic side, and we find that glucose is quite soluble in water.
We saw that ethanol was very water-soluble (if it were not, drinking beer or vodka would be rather inconvenient!) How about
dimethyl ether, which is a constitutional isomer of ethanol but with an ether rather than an alcohol functional group? We find that
diethyl ether is much less soluble in water. Is it capable of forming hydrogen bonds with water? Yes, in fact, it is –the ether oxygen
can act as a hydrogen-bond acceptor. The difference between the ether group and the alcohol group, however, is that the alcohol
group is both a hydrogen bond donor and acceptor.

The result is that the alcohol is able to form more energetically favorable interactions with the solvent compared to the ether, and
the alcohol is therefore more soluble.
Here is another easy experiment that can be done (with proper supervision) in an organic laboratory. Try dissolving benzoic acid
crystals in room temperature water – you'll find that it is not soluble. As we will learn when we study acid-base chemistry in a later
chapter, carboxylic acids such as benzoic acid are relatively weak acids, and thus exist mostly in the acidic (protonated) form when
added to pure water.

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Acetic acid, however, is quite soluble. This is easy to explain using the small alcohol vs large alcohol argument: the hydrogen-
bonding, hydrophilic effect of the carboxylic acid group is powerful enough to overcome the hydrophobic effect of a single methyl
group on acetic acid, but not the larger hydrophobic effect of the 6-carbon benzene group on benzoic acid.
Now, try slowly adding some aqueous sodium hydroxide to the flask containing undissolved benzoic acid. As the solvent becomes
more and more basic, the benzoic acid begins to dissolve, until it is completely in solution.

What is happening here is that the benzoic acid is being converted to its conjugate base, benzoate. The neutral carboxylic acid
group was not hydrophilic enough to make up for the hydrophobic benzene ring, but the carboxylate group, with its full negative
charge, is much more hydrophilic. Now, the balance is tipped in favor of water solubility, as the powerfully hydrophilic anion part
of the molecule drags the hydrophobic part, kicking and screaming, (if a benzene ring can kick and scream) into solution. If you
want to precipitate the benzoic acid back out of solution, you can simply add enough hydrochloric acid to neutralize the solution
and reprotonate the carboxylate.
If you are taking a lab component of your organic chemistry course, you will probably do at least one experiment in which you will
use this phenomenon to separate an organic acid like benzoic acid from a hydrocarbon compound like biphenyl.
Similar arguments can be made to rationalize the solubility of different organic compounds in nonpolar or slightly polar solvents. In
general, the greater the content of charged and polar groups in a molecule, the less soluble it tends to be in solvents such as hexane.
The ionic and very hydrophilic sodium chloride, for example, is not at all soluble in hexane solvent, while the hydrophobic
biphenyl is very soluble in hexane.

Example

Exercise 2.12: Vitamins can be classified as water-soluble or fat-soluble (consider fat to be a very non-polar, hydrophobic 'solvent'. Decide on a
classification for each of the vitamins shown below.

Exercise 2.13: Both aniline and phenol are insoluble in pure water. Predict the solubility of these two compounds in 10% aqueous hydrochloric
acid, and explain your reasoning. Hint – in this context, aniline is basic, phenol is not!

Solutions

Illustrations of solubility concepts: metabolic intermediates, lipid bilayer membranes, soaps and
detergents
Because water is the biological solvent, most biological organic molecules, in order to maintain water-solubility, contain one or
more charged functional groups. These are most often phosphate, ammonium or carboxylate, all of which are charged when
dissolved in an aqueous solution buffered to pH 7.

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Sugars often lack charged groups, but as we discussed in our ‘thought experiment’ with glucose, they are quite water-soluble due to
the presence of multiple hydroxyl groups.
Some biomolecules, in contrast, contain distinctly hydrophobic components. The ‘lipid bilayer’ membranes of cells and subcellular
organelles serve to enclose volumes of water and myriad biomolecules in solution. The lipid (fat) molecules that make up
membranes are amphipathic: they have a charged, hydrophilic ‘head’ and a hydrophobic hydrocarbon ‘tail’.

interactive 3D image of a membrane phospholipid (BioTopics)

Notice that the entire molecule is built on a ‘backbone’ of glycerol, a simple 3-carbon molecule with three alcohol groups. In a
biological membrane structure, lipid molecules are arranged in a spherical bilayer: hydrophobic tails point inward and bind together
by van der Waals forces, while the hydrophilic head groups form the inner and outer surfaces in contact with water.

Interactive 3D Image of a lipid bilayer (BioTopics)

Because the interior of the bilayer is extremely hydrophobic, biomolecules (which as we know are generally charged species) are
not able to diffuse through the membrane– they are simply not soluble in the hydrophobic interior. The transport of molecules
across the membrane of a cell or organelle can therefore be accomplished in a controlled and specific manner by special
transmembrane transport proteins, a fascinating topic that you will learn more about if you take a class in biochemistry.
A similar principle is the basis for the action of soaps and detergents. Soaps are composed of fatty acids, which are long (typically
18-carbon), hydrophobic hydrocarbon chains with a (charged) carboxylate group on one end,

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Fatty acids are derived from animal and vegetable fats and oils. In aqueous solution, the fatty acid molecules in soaps will
spontaneously form micelles, a spherical structure that allows the hydrophobic tails to avoid contact with water and simultaneously
form favorable van der Waals contacts.

Interactive 3D images of a fatty acid soap molecule and a soap micelle (Edutopics)
Because the outside of the micelle is charged and hydrophilic, the structure as a whole is soluble in water. Micelles will form
spontaneously around small particles of oil that normally would not dissolve in water (like that greasy spot on your shirt from the
pepperoni slice that fell off your pizza), and will carry the particle away with it into solution. We will learn more about the
chemistry of soap-making in a later chapter (section 12.4B).
Synthetic detergents are non-natural amphipathic molecules that work by the same principle as that described for soaps.

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

Hydrogen Bonding and Solubility

The physical properties of alcohols are influenced by the hydrogen bonding ability of the -OH group. The -OH groups can
hydrogen bond with one another and with other molecules.

Hydrogen Bonding of Methanol

Hydrogen bonding raises the boiling point of alcohols. This is due to the combined strength of so many hydrogen bonds forming
between oxygen atoms of one alcohol molecule and the hydroxy H atoms of another. The longer the carbon chain in an alcohol is,
the lower the solubility in polar solvents and the higher the solubility in nonpolar solvents.
Physical Properties of Alchols and Selected Analogous Haloalkanes and Alkanes
Solubility in H2O at
Compound IUPAC Name Common Name Melting Poing (oC) Boiling Point (oC)
23oC

CH3OH Methanol Methyl alcohol -97.8 65.0 Infinite

CH3Cl Chloromethane Methyl chloride -97.7 -24.2 0.74 g/100 mL

CH4 Methane -182.5 -161.7 3.5 mL (gas)/ 100 mL

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 CH3CH2OH Ethanol Ethyl alcohol -114.7 78.5 Infinite

CH3CH2Cl Chloroethane Ethyl chloride -136.4 12.3 0.447 g/100 mL

CH3CH3 Ethane -183.3 -88.6 4.7 mL (gas)/ 100 mL

CH3CH2CH2OH 1-Propanol Propyl alcohol -126.5 97.4 Infinite

CH3CH2CH3 Propane -187.7 -42.1 6.5 mL (gas)/ 100 mL

CH3CH2CH2CH2OH 1-Butanol Butyl alcohol -89.5 117.3 8.0 g/100 mL

CH3(CH2)4OH 1-Pentanol Pentyl alcohol -79 138 2.2 g/100 mL

This table shows that alcohols (in red) have higher boiling points and greater solubility in H2O than haloalkanes and alkanes with
the same number of carbons. It also shows that the boiling point of alcohols increase with the number of carbon atoms.

References
1. Schore, Neil E. and Vollhardt, K. Peter C. Organic Chemistry: Structure and Function. New York: Bleyer, Brennan, 2007.
2. Allen, Frank; Kennard. Olga; Watson, David G.; Brammer, Lee; Orpen, Guy; Taylor, Robin, J. Chem Soc. Perkin Trans II,
1987,S1-S19.

Outside Links
http://en.wikipedia.org/wiki/Alcohol#Physical_and_chemical_properties
http://www.chemguide.co.uk/organicprops/alcohols/background.html

Problems
Arrange according to increasing boiling point. (start with lowest boiling point)
1. CH4, CH3OH, CH3CH3
2. CH3CH2Cl, CH3CH2CH2OH, CH3CH2CH3
3. CH3CH2OH, CH3CH2Cl, CH4
Arrange according to increasing solubility (start with lowest solubility)
4. CH4, CH3OH, CH3CH3
5. CH4, CH3CH2Cl, CH3CH2OH,
6. CH3CH2Cl, CH3CH2CH2OH, CH3CH2CH3

Answers
1. CH4, CH3CH3, CH3OH
2. CH3CH2CH3, CH3CH2Cl, CH3CH2CH2OH
3. CH3CH2Cl, CH4, CH3CH2OH
4. CH3CH3, CH4, CH3OH
5. CH3CH2Cl, CH4, CH3CH2OH,
6. CH3CH2Cl, CH3CH2CH3, CH3CH2CH2OH

Contributors
Jaspreet Dheri

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4.5 Chromatography
The main chromatographic techniques (thin layer chromatography, column chromatography, and gas chromatography) follow the
same general principles in terms of how they are able to separate mixtures.
In all chromatographic methods, a sample is first applied onto a stationary material that either absorbs or adsorbs the sample:
adsorption is when molecules or ions in a sample adhere to a surface, while absorption is when the sample particles penetrate into
the interior of another material. A paper towel absorbs water because the water molecules form intermolecular forces (in this case
hydrogen bonds) with the cellulose in the paper towel. In chromatography, a sample is typically adsorbed onto a surface, and can
form a variety of intermolecular forces with this surface.
After adsorption, the sample is then exposed to a liquid or gas traveling in one direction. The sample may overcome its
intermolecular forces with the stationary surface and transfer into the moving material, due to some attraction or sufficient thermal
energy. The sample will later readsorb to the stationary material, and transition between the two materials in a constant equilibrium
(Equation 1). If there is to be any separation between components in a mixture, it is crucial that there are many equilibrium "steps"
in the process (summarized in Figure 2.3).

X(stationary) ⇋ X(mobile) (1)

The material the sample adsorbs onto is referred to as the "stationary phase" because it retains the sample's position. The moving
material is called the "mobile phase" because it can cause the sample to move from its original position.

Figure 2.3: Generic chromatography sequence for compound X: a) Adsorption, b) Exposure to a mobile phase, c) Sample X breaks
its attachment to the stationary phase, d) Movement with the mobile phase, e) Reattachment to the stationary phase. Steps c-e are
equilibrium steps and constantly repeated.
The main principle that allows chromatography to separate components of a mixture is that components will spend different
amounts of time interacting with the stationary and mobile phases. A compound that spends a large amount of time mobile will
move quickly away from its original location, and will separate from a compound that spends a larger amount of time stationary.
The main principle that determines the amount of time spent in the phases is the strength of intermolecular forces experienced in
each phase. If a compound has strong intermolecular forces with the stationary phase it will remain adsorbed for a longer amount of
time than a compound that has weaker intermolecular forces. This causes compounds with different strengths of intermolecular
forces to move at different rates.
How these general ideas apply to each chromatographic technique (thin layer chromatography, column chromatography, and gas
chromatography) will be explained in greater detail in each section.

Contributor
Lisa Nichols (Butte Community College). Organic Chemistry Laboratory Techniques is licensed under a Creative Commons
Attribution-NonCommercial-NoDerivatives 4.0 International License. Complete text is available online.

4.5 Chromatography is shared under a not declared license and was authored, remixed, and/or curated by LibreTexts.

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 CHAPTER OVERVIEW

Chapter 5. Spectroscopy

Purdue CHM 26505: Organic

Chemistry for Chemistry Majors (1st
Semester)
Fall 2014: Prof. Mark Lipton

Template:HideTOC

Topic hierarchy
5.1 Infrared Spectroscopy
5.2 Mass Spectrometry
5.3 Nuclear Magnetic Resonance (NMR) Spectroscopy
5.4 Ultraviolet (UV) Spectroscopy
5.5 Polarimetry

Chapter 5. Spectroscopy is shared under a CC BY-NC-SA 4.0 license and was authored, remixed, and/or curated by LibreTexts.

1
5.1 Infrared Spectroscopy
The light our eyes see is but a small part of a broad spectrum of electromagnetic radiation. On the immediate high energy side of
the visible spectrum lies the ultraviolet, and on the low energy side is the infrared. The portion of the infrared region most useful
for analysis of organic compounds is not immediately adjacent to the visible spectrum, but is that having a wavelength range from
2,500 to 16,000 nm, with a corresponding frequency range from 1.9*1013 to 1.2*1014 Hz.

Introduction
Photon energies associated with this part of the infrared (from 1 to 15 kcal/mole) are not large enough to excite electrons, but may
induce vibrational excitation of covalently bonded atoms and groups.

The covalent bonds in molecules are not rigid sticks or rods, such as found in molecular model kits, but are more like stiff springs
that can be stretched and bent. The mobile nature of organic molecules was noted in the chapter concerning conformational
isomers. We must now recognize that, in addition to the facile rotation of groups about single bonds, molecules experience a wide
variety of vibrational motions, characteristic of their component atoms. Consequently, virtually all organic compounds will absorb
infrared radiation that corresponds in energy to these vibrations. Infrared spectrometers, similar in principle to the UV-Visible
spectrometer described elsewhere, permit chemists to obtain absorption spectra of compounds that are a unique reflection of their
molecular structure. An example of such a spectrum is that of the flavoring agent vanillin, shown below.

The complexity of this spectrum is typical of most infrared spectra, and illustrates their use in identifying substances. The gap in
the spectrum between 700 & 800 cm-1 is due to solvent (CCl4) absorption. Further analysis (below) will show that this spectrum
also indicates the presence of an aldehyde function, a phenolic hydroxyl and a substituted benzene ring. The inverted display of
absorption, compared with UV-Visible spectra, is characteristic. Thus a sample that did not absorb at all would record a horizontal
line at 100% transmittance (top of the chart).
The frequency scale at the bottom of the chart is given in units of reciprocal centimeters (cm-1) rather than Hz, because the
numbers are more manageable. The reciprocal centimeter is the number of wave cycles in one centimeter; whereas, frequency in
cycles per second or Hz is equal to the number of wave cycles in 3*1010 cm (the distance covered by light in one second).
Wavelength units are in micrometers, microns (μ), instead of nanometers for the same reason. Most infrared spectra are displayed
on a linear frequency scale, as shown here, but in some older texts a linear wavelength scale is used. A calculator for
interconverting these frequency and wavelength values is provided on the right. Simply enter the value to be converted in the
appropriate box, press "Calculate" and the equivalent number will appear in the empty box.
Infrared spectra may be obtained from samples in all phases (liquid, solid and gaseous). Liquids are usually examined as a thin film
sandwiched between two polished salt plates (note that glass absorbs infrared radiation, whereas NaCl is transparent). If solvents
are used to dissolve solids, care must be taken to avoid obscuring important spectral regions by solvent absorption. Perchlorinated
solvents such as carbon tetrachloride, chloroform and tetrachloroethene are commonly used. Alternatively, solids may either be
incorporated in a thin KBr disk, prepared under high pressure, or mixed with a little non-volatile liquid and ground to a paste (or
mull) that is smeared between salt plates.

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 Frequency - Wavelength Converter

Frequency in cm-1
Calculate
Wavelength in μ

Vibrational Spectroscopy
A molecule composed of n-atoms has 3n degrees of freedom, six of which are translations and rotations of the molecule itself. This
leaves 3n-6 degrees of vibrational freedom (3n-5 if the molecule is linear). Vibrational modes are often given descriptive names,
such as stretching, bending, scissoring, rocking and twisting. The four-atom molecule of formaldehyde, the gas phase spectrum of
which is shown below, provides an example of these terms. If a ball & stick model of formaldehyde is not displayed to the right of
the spectrum, press the view ball&stick model button on the right. We expect six fundamental vibrations (12 minus 6), and these
have been assigned to the spectrum absorptions. To see the formaldehyde molecule display a vibration, click one of the buttons
under the spectrum, or click on one of the absorption peaks in the spectrum.

r…
Gas Phase Infrared Spectrum of Formaldehyde, H2C=O
Click Here. In practice, infrared spectra do not
normally display separate absorption signals
for each of the 3n-6 fundamental vibrational
modes of a molecule. The number of observed
absorptions may be increased by additive and
subtractive interactions leading to combination
tones and overtones of the fundamental
vibrations, in much the same way that sound
vibrations from a musical instrument interact.
Furthermore, the number of observed
absorptions may be decreased by molecular
symmetry, spectrometer limitations, and
spectroscopic selection rules. One selection
rule that influences the intensity of infrared
absorptions, is that a change in dipole moment
should occur for a vibration to absorb infrared
energy. Absorption bands associated with C=O
bond stretching are usually very strong because
a large change in the dipole takes place in that
mode.
Some General Trends:
1. Stretching frequencies are higher than
corresponding bending frequencies. (It is
easier to bend a bond than to stretch or
compress it.)
2. Bonds to hydrogen have higher stretching
frequencies than those to heavier atoms.
3. Triple bonds have higher stretching
frequencies than corresponding double
bonds, which in turn have higher
frequencies than single bonds.(Except for
bonds to hydrogen).
The general regions of the infrared spectrum in
which various kinds of vibrational bands are
observed are outlined in the following chart.
Note that the blue colored sections above the
dashed line refer to stretching vibrations, and
the green colored band below the line

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encompasses bending vibrations. The
complexity of infrared spectra in the 1450 to
600 cm-1 region makes it difficult to assign all
the absorption bands, and because of the
unique patterns found there, it is often called
the fingerprint region. Absorption bands in
the 4000 to 1450 cm-1 region are usually due to
stretching vibrations of diatomic units, and this
is sometimes called the group frequency
region.

Group Frequencies
Detailed information about the infrared
absorptions observed for various bonded atoms
and groups is usually presented in tabular
form. The following table provides a collection
of such data for the most common functional
groups. Following the color scheme of the
chart, stretching absorptions are listed in the
blue-shaded section and bending absorptions in
the green shaded part. More detailed
descriptions for certain groups (e.g. alkenes,
arenes, alcohols, amines & carbonyl
compounds) may be viewed by clicking on
the functional class name. Since most organic
compounds have C-H bonds, a useful rule is
that absorption in the 2850 to 3000 cm-1 is due
to sp3 C-H stretching; whereas, absorption
above 3000 cm-1 is from sp2 C-H stretching or
sp C-H stretching if it is near 3300 cm-1.

Typical Infrared Absorption

Frequencies
Stretching
Bending Vibrations
Vibrations
Func Rang
Assig Assig
tiona e Inten Inten
-
nmen Range (cm-1) nmen
l (cm sity sity
t t
Class 1)

1350
-
285 1470
med CH2 & CH3 deformation
Alk 0- CH3, CH 1370
2 & CH
str med CH3 deformation
anes 300 2 or 3 bands
-
wk CH2 rocking
0 1390
720-
725

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 302 =C-H
0- &
310 =CH
0 2
880-
163 (out-
med =C-H &995
=CH2 (usually sharp)
0- str of-
Alk var C=C (symmetry
780- reduces intensity)
168 med plane
enes 850
0 med bendi
str C=C asymmetric
675- stretch
ng)
730
190 cis-
0- RCH
200 =CH
0 R

C-H
(usu
ally
shar
330
p)
0 C-H
C≡C
Alk 210 str 600- defor
(sym str
ynes 0- var 700 matio
metr
225 n
y
0
redu
ces
inten
sity)

303 C-H
0 bendi
var C-H (may be several bands)
Are 160 690- str- ng &
med C=C (in ring) (2 bands)
nes 0& 900 med ring
-wk (3 if conjugated)
150 puck
0 ering

O-H
(free
), O-H
358
usua bendi
0-
lly ng
365
shar (in-
Alco 0 1330
p plane
hols 320 var - med
O-H )
& 0- str 1430 var-
(H- O-H
Phe 355 str 650- wk
bond bend
nols 0 770
ed), (out-
970-
usua of-
125
lly plane
0
broa )
d
C-O

340
0- NH2
350 sciss
0 oring
(dil. (1°-
soln. amin
) es)
1550
330 NH
wk N-H (1°-amines),
- med-2 bands 2
Ami 0- & N-
wk N-H (2°-amines)
1650 str
nes 340 H
med C-N 660- var
0 wagg
900
(dil. ing
soln. (shift
) s on
100 H-
0- bondi
125 ng)
0

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Ald
ehy
2690-2840(2 bands)
des
1720-1740
&
1710-1720
Ket
ones

C-H
(ald
ehyd
e C-
H)
C=O
(satu
rate
d
alde
hyde
)
α-
C=O
CH3
med (satu 135
bendi
str rate 0-
ng
str d 136
α-
keto 0 str
CH2
str ne) 140 str
bendi
str 0- med
ng
str aryl 145
C-C-
str keto 0
C
ne 1100
bendi
α, β-
ng
unsa
turat
ion
cycl
open
tano
ne
cycl
obut
anon
e

Car
box
ylic
Aci 2500-3300 (acids) overlap C-H
ds 1705-1720 (acids)
& 1210-1320 (acids)
Deri
vati
ves

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 O-H
(ver
y
broa
d)
C=O
(H- C-O-
bon 139 H
ded) 5- bendi
O-C 144 ng
(so 0
str meti
med
str mes
med 2-
-str peak
s)
str
str C=O N-H
str C=O 159 (1°-
str (2- 0- amid
med
str band 165 e) II
med
str s) 0 band
O-C 150 N-H
C=O 0- (2°-
O-C 156 amid
(2- 0 e) II
band band
s)
C=O
(ami
de I
band
)

Nitr
iles C≡N
(shar
Isoc p)
yan
224
ates, -
0-
Isot N=C
226
hioc =O,
0 med
yan -
ates, N=C
210 med
Dii =S
0-
mid -
227
es, N=C
0
Azi =N-,
des -N3,
& C=C
Ket =O
enes

To illustrate the usefulness of infrared

absorption spectra, examples for five C4H8O
isomers are presented below their
corresponding structural formulas. Try to
associate each spectrum (A - E) with one of the
isomers in the row above it.Answers

Other Functional Groups

Infrared absorption data for some functional
groups not listed in the preceding table are
given below. Most of the absorptions cited are
associated with stretching vibrations. Standard
abbreviations (str = strong, wk = weak, brd =

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 broad & shp = sharp) are used to describe the
absorption bands.
Functional Class Characteristic Absorptions
Sulfur Functions

S-H thiols 2550-2600 cm-1 (wk & shp)

S-OR esters 700-900 (str)

S-S disulfide 500-540 (wk)

C=S thiocarbonyl 1050-1200 (str)

S=O sulfoxide
1030-1060 (str)
1325± 25 (as) & 1140± 20 (s) (both str)
1345 (str)
1365± 5 (as) & 1180± 10 (s) (both str)
1350-1450 (str)
Phosphorous Functions
2280-2440 cm-1 (med & shp)
P-H phosphine
950-1250 (wk) P-H bending
(O=)PO-H phosphonic acid 2550-2700 (med)

P-OR esters 900-1050 (str)

P=O phosphine oxide
1100-1200 (str)
1230-1260 (str)
1100-1200 (str)
1200-1275 (str)
Silicon Functions

Si-H silane 2100-2360 cm-1 (str)

Si-OR 1000-1110 (str & brd)

Si-CH3 1250± 10 (str & shp)

Oxidized Nitrogen Functions
=NOH oxime

3550-3600 cm-1 (str)

1665± 15
945± 15
N-O amine oxide

960± 20
1250± 50
N=O nitroso
1550± 50 (str)
1530± 20 (as) & 1350± 30 (s)

Internal Links
Organic Chemistry With a Biological
Emphasis

Contributors
William Reusch, Professor Emeritus
(Michigan State U.), Virtual Textbook
of Organic Chemistry

5.1 Infrared Spectroscopy is shared under a CC BY-NC-SA 4.0 license and was authored, remixed, and/or curated by LibreTexts.
Infrared Spectroscopy by William Reusch is licensed CC BY-NC-SA 4.0.

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5.2 Mass Spectrometry
The Mass Spectrometer
In order to measure the characteristics of individual molecules, a mass spectrometer converts them to ions so that they can be moved about and manipulated by external electric and magnetic fields.
The three essential functions of a mass spectrometer, and the associated components, are:
1. A small sample is ionized, usually to cations by loss of an electron. The Ion Source
2. The ions are sorted and separated according to their mass and charge. The Mass Analyzer
3. The separated ions are then measured, and the results displayed on a chart. The Detector
Because ions are very reactive and short-lived, their formation and manipulation must be conducted in a vacuum. Atmospheric pressure is around 760 torr (mm of mercury). The pressure under which
ions may be handled is roughly 10-5 to 10-8 torr (less than a billionth of an atmosphere). Each of the three tasks listed above may be accomplished in different ways. In one common procedure,
ionization is effected by a high energy beam of electrons, and ion separation is achieved by accelerating and focusing the ions in a beam, which is then bent by an external magnetic field. The ions are
then detected electronically and the resulting information is stored and analyzed in a computer. A mass spectrometer operating in this fashion is outlined in the following diagram. The heart of the
spectrometer is the ion source. Here molecules of the sample (black dots) are bombarded by electrons (light blue lines) issuing from a heated filament. This is called an EI (electron-impact) source.
Gases and volatile liquid samples are allowed to leak into the ion source from a reservoir (as shown). Non-volatile solids and liquids may be introduced directly. Cations formed by the electron
bombardment (red dots) are pushed away by a charged repellor plate (anions are attracted to it), and accelerated toward other electrodes, having slits through which the ions pass as a beam. Some of
these ions fragment into smaller cations and neutral fragments. A perpendicular magnetic field deflects the ion beam in an arc whose radius is inversely proportional to the mass of each ion. Lighter
ions are deflected more than heavier ions. By varying the strength of the magnetic field, ions of different mass can be focused progressively on a detector fixed at the end of a curved tube (also under a
high vacuum).

When a high energy electron collides with a molecule it often ionizes it by knocking away one of the molecular electrons (either bonding or non-bonding). This leaves behind a molecular ion
(colored red in the following diagram). Residual energy from the collision may cause the molecular ion to fragment into neutral pieces (colored green) and smaller fragment ions (colored pink and
orange). The molecular ion is a radical cation, but the fragment ions may either be radical cations (pink) or carbocations (orange), depending on the nature of the neutral fragment. An animated
display of this ionization process will appear if you click on the ion source of the mass spectrometer diagram.

The Nature of Mass Spectra

A mass spectrum will usually be presented as a vertical bar graph, in which each bar represents an ion having a specific mass-to-charge ratio (m/z) and the length of the bar indicates the relative
abundance of the ion. The most intense ion is assigned an abundance of 100, and it is referred to as the base peak. Most of the ions formed in a mass spectrometer have a single charge, so the m/z
value is equivalent to mass itself. Modern mass spectrometers easily distinguish (resolve) ions differing by only a single atomic mass unit, and thus provide completely accurate values for the
molecular mass of a compound. The highest-mass ion in a spectrum is normally considered to be the molecular ion, and lower-mass ions are fragments from the molecular ion, assuming the sample is
a single pure compound.
Atomic mass is given in terms of the unified atomic mass unit (symbol: μ) or dalton (symbol: Da). In recent years there has been a gradual change towards using the dalton in preference to the
unified atomic mass unit. The dalton is classified as a "non-SI unit whose values in SI units must be obtained experimentally". It is defined as one twelfth of the rest mass of an unbound atom of
carbon-12 in its nuclear and electronic ground state, and has a value of 1.660538782(83)x10-27 kg.
The following diagram displays the mass spectra of three simple gaseous compounds, carbon dioxide, propane and cyclopropane. The molecules of these compounds are similar in size, CO2 and C3H8
both have a nominal mass of 44 Da, and C3H6 has a mass of 42 Da. The molecular ion is the strongest ion in the spectra of CO2 and C3H6, and it is moderately strong in propane. The unit mass
resolution is readily apparent in these spectra (note the separation of ions having m/z=39, 40, 41 and 42 in the cyclopropane spectrum). Even though these compounds are very similar in size, it is a
simple matter to identify them from their individual mass spectra. By clicking on each spectrum in turn, a partial fragmentation analysis and peak assignment will be displayed. Even with simple
compounds like these, it should be noted that it is rarely possible to explain the origin of all the fragment ions in a spectrum. Also, the structure of most fragment ions is seldom known with certainty.

Since a molecule of carbon dioxide is composed of only three atoms, its mass spectrum is very simple. The molecular ion is also the base peak, and the only fragment ions are CO (m/z=28) and O
(m/z=16). The molecular ion of propane also has m/z=44, but it is not the most abundant ion in the spectrum. Cleavage of a carbon-carbon bond gives methyl and ethyl fragments, one of which is a
carbocation and the other a radical. Both distributions are observed, but the larger ethyl cation (m/z=29) is the most abundant, possibly because its size affords greater charge dispersal. A similar bond

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 cleavage in cyclopropane does not give two fragments, so the molecular ion is stronger than in propane, and is in fact responsible for the the base peak. Loss of a hydrogen atom, either before or after
ring opening, produces the stable allyl cation (m/z=41). The third strongest ion in the spectrum has m/z=39 (C3H3). Its structure is uncertain, but two possibilities are shown in the diagram. The small
m/z=39 ion in propane and the absence of a m/z=29 ion in cyclopropane are particularly significant in distinguishing these hydrocarbons.
Most stable organic compounds have an even number of total electrons, reflecting the fact that electrons occupy atomic and molecular orbitals in pairs. When a single electron is removed from a
molecule to give an ion, the total electron count becomes an odd number, and we refer to such ions as radical cations. The molecular ion in a mass spectrum is always a radical cation, but the
fragment ions may either be even-electron cations or odd-electron radical cations, depending on the neutral fragment lost. The simplest and most common fragmentations are bond cleavages
producing a neutral radical (odd number of electrons) and a cation having an even number of electrons. A less common fragmentation, in which an even-electron neutral fragment is lost, produces an
odd-electron radical cation fragment ion. Fragment ions themselves may fragment further. As a rule, odd-electron ions may fragment either to odd or even-electron ions, but even-electron ions
fragment only to other even-electron ions. The masses of molecular and fragment ions also reflect the electron count, depending on the number of nitrogen atoms in the species.

Ions with no nitrogen odd-electron ions even-electron ions

or an even # N atoms even-number mass odd-number mass

Ions having an odd-electron ions even-electron ions

odd # N atoms odd-number mass even-number mass

This distinction is illustrated nicely by the follwing two examples. The unsaturated ketone, 4-methyl-3-pentene-2-one, on the left has no nitrogen so the mass of the molecular ion (m/z = 98) is an even
number. Most of the fragment ions have odd-numbered masses, and therefore are even-electron cations. Diethylmethylamine, on the other hand, has one nitrogen and its molecular mass (m/z = 87) is
an odd number. A majority of the fragment ions have even-numbered masses (ions at m/z = 30, 42, 56 & 58 are not labeled), and are even-electron nitrogen cations. The weak even -electron ions at
m/z=15 and 29 are due to methyl and ethyl cations (no nitrogen atoms). The fragmentations leading to the chief fragment ions will be displayed by clicking on the appropriate spectrum. Repeated
clicks will cycle the display.

4-methyl-3-pentene-2-one N,N-diethylmethylamine

When non-bonded electron pairs are present in a molecule (e.g. on N or O), fragmentation pathways may sometimes be explained by assuming the missing electron is partially localized on that atom.
A few such mechanisms are shown above. Bond cleavage generates a radical and a cation, and both fragments often share these roles, albeit unequally.

Isotopes
Since a mass spectrometer separates and detects ions of slightly different masses, it easily distinguishes different isotopes of a given element. This is manifested most dramatically for compounds
containing bromine and chlorine, as illustrated by the following examples. Since molecules of bromine have only two atoms, the spectrum on the left will come as a surprise if a single atomic mass of
80 Da is assumed for Br. The five peaks in this spectrum demonstrate clearly that natural bromine consists of a nearly 50:50 mixture of isotopes having atomic masses of 79 and 81 Da respectively.
Thus, the bromine molecule may be composed of two 79Br atoms (mass 158 Da), two 81Br atoms (mass 162 Da) or the more probable combination of 79Br-81Br (mass 160 Da). Fragmentation of Br2
to a bromine cation then gives rise to equal sized ion peaks at 79 and 81 Da.

bromine vinyl chloride methylene chloride

The center and right hand spectra show that chlorine is also composed of two isotopes, the more abundant having a mass of 35 Da, and the minor isotope a mass 37 Da. The precise isotopic
composition of chlorine and bromine is:
Chlorine: 75.77% 35Cl and 24.23% 37Cl
Bromine: 50.50% 79Br and 49.50% 81Br
The presence of chlorine or bromine in a molecule or ion is easily detected by noticing the intensity ratios of ions differing by 2 Da. In the case of methylene chloride, the molecular ion consists of
three peaks at m/z=84, 86 & 88 Da, and their diminishing intensities may be calculated from the natural abundances given above. Loss of a chlorine atom gives two isotopic fragment ions at m/z=49
& 51 Da, clearly incorporating a single chlorine atom. Fluorine and iodine, by contrast, are monoisotopic, having masses of 19 Da and 127 Da respectively. It should be noted that the presence of
halogen atoms in a molecule or fragment ion does not change the odd-even mass rules given above.
To make use of a calculator that predicts the isotope clusters for different combinations of chlorine, bromine and other elements Click Here. This application was developed at Colby College.
Two
other Isotopic Abundance Calculator
com C H
mon
M + 1 M + 2
eleme
opic Abund… Molecular Ion
100%
nts
havin
g
usefu
l isotope signatures are carbon, 13C is 1.1% natural abundance, and sulfur, 33S and 34S are 0.76% and 4.22% natural abundance respectively. For example, the small m/z=99 Da peak in the spectrum of
4-methyl-3-pentene-2-one (above) is due to the presence of a single 13C atom in the molecular ion. Although less important in this respect, 15N and 18O also make small contributions to higher mass
satellites of molecular ions incorporating these elements.

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The calculator on the right may be used to calculate the isotope contributions to ion abundances 1 and 2 Da greater than the molecular ion (M). Simply enter an appropriate subscript number to the
right of each symbol, leaving those elements not present blank, and press the "Calculate" button. The numbers displayed in the M+1 and M+2 boxes are relative to M being set at 100%.

Fragmentation Patterns
The fragmentation of molecular ions into an assortment of fragment ions is a mixed blessing. The nature of the fragments often provides a clue to the molecular structure, but if the molecular ion has a
lifetime of less than a few microseconds it will not survive long enough to be observed. Without a molecular ion peak as a reference, the difficulty of interpreting a mass spectrum increases markedly.
Fortunately, most organic compounds give mass spectra that include a molecular ion, and those that do not often respond successfully to the use of milder ionization conditions. Among simple organic
compounds, the most stable molecular ions are those from aromatic rings, other conjugated pi-electron systems and cycloalkanes. Alcohols, ethers and highly branched alkanes generally show the
greatest tendency toward fragmentation.

The mass spectrum of dodecane on the right illustrates the behavior of an unbranched alkane. Since there are no heteroatoms in this molecule, there are no non-bonding valence shell electrons.
Consequently, the radical cation character of the molecular ion (m/z = 170) is delocalized over all the covalent bonds. Fragmentation of C-C bonds occurs because they are usually weaker than C-H
bonds, and this produces a mixture of alkyl radicals and alkyl carbocations. The positive charge commonly resides on the smaller fragment, so we see a homologous series of hexyl (m/z = 85), pentyl
(m/z = 71), butyl (m/z = 57), propyl (m/z = 43), ethyl (m/z = 29) and methyl (m/z = 15) cations. These are accompanied by a set of corresponding alkenyl carbocations (e.g. m/z = 55, 41 &27) formed
by loss of 2 H. All of the significant fragment ions in this spectrum are even-electron ions. In most alkane spectra the propyl and butyl ions are the most abundant.
The presence of a functional group, particularly one having a heteroatom Y with non-bonding valence electrons (Y = N, O, S, X etc.), can dramatically alter the fragmentation pattern of a compound.
This influence is thought to occur because of a "localization" of the radical cation component of the molecular ion on the heteroatom. After all, it is easier to remove (ionize) a non-bonding electron
than one that is part of a covalent bond. By localizing the reactive moiety, certain fragmentation processes will be favored. These are summarized in the following diagram, where the green shaded
box at the top displays examples of such "localized" molecular ions. The first two fragmentation paths lead to even-electron ions, and the elimination (path #3) gives an odd-electron ion. Note the use
of different curved arrows to show single electron shifts compared with electron pair shifts.

The charge distributions shown above are common, but for each cleavage process the charge may sometimes be carried by the other (neutral) species, and both fragment ions are observed. Of the
three cleavage reactions described here, the alpha-cleavage is generally favored for nitrogen, oxygen and sulfur compounds. Indeed, in the previously displayed spectra of 4-methyl-3-pentene-2-one
and N,N-diethylmethylamine the major fragment ions come from alpha-cleavages. Further examples of functional group influence on fragmentation are provided by a selection of compounds that
may be examined by clicking the left button below. Useful tables of common fragment ions and neutral species may be viewed by clicking the right button.

Assorted Mass Spectra View Fragment Tables

The complexity of fragmentation patterns has led to mass spectra being used as "fingerprints" for identifying compounds. Environmental pollutants, pesticide residues on food, and controlled
substance identification are but a few examples of this application. Extremely small samples of an unknown substance (a microgram or less) are sufficient for such analysis. The following mass
spectrum of cocaine demonstrates how a forensic laboratory might determine the nature of an unknown street drug. Even though extensive fragmentation has occurred, many of the more abundant
ions (identified by magenta numbers) can be rationalized by the three mechanisms shown above. Plausible assignments may be seen by clicking on the spectrum, and it should be noted that all are
even-electron ions. The m/z = 42 ion might be any or all of the following: C3H6, C2H2O or C2H4N. A precise assignment could be made from a high-resolution m/z value (next section).

Odd-electron fragment ions are often formed by characteristic rearrangements in which stable neutral fragments are lost. Mechanisms for some of these rearrangements have been identified by
following the course of isotopically labeled molecular ions. A few examples of these rearrangement mechanisms may be seen by clicking the following button.

Assorted Rearrangement Fragmentations

High Resolution Mass Spectrometry

In assigning mass values to atoms and molecules, we have assumed integral values for isotopic masses. However, accurate measurements show that this is not strictly true. Because the strong nuclear
forces that bind the components of an atomic nucleus together vary, the actual mass of a given isotope deviates from its nominal integer by a small but characteristic amount (remember E = mc2).
Thus, relative to 12C at 12.0000, the isotopic mass of 16O is 15.9949 Da (not 16) and 14N is 14.0031 Da (not 14).
By Formula C6H12 C5H8O C4H8N2
desig
Mass 84.0939 84.0575 84.0688
ning
mass
spectrometers that can determine m/z values accurately to four decimal places, it is possible to distinguish different formulas having the same nominal mass. The table on the right illustrates this
important feature, and a double-focusing high-resolution mass spectrometer easily distinguishes ions having these compositions. Mass spectrometry therefore not only provides a specific molecular
mass value, but it may also establish the molecular formula of an unknown compound.
Tables of precise mass values for any molecule or ion are available in libraries; however, the mass calculator provided below serves the same purpose. Since a given nominal mass may correspond to

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several molecular formulas, lists of such possibilities are especially useful when evaluating the spectrum of an unknown compound. Composition tables are available for this purpose, and a
particularly useful program for calculating all possible combinations of H, C, N & O that give a specific nominal mass has been written by Jef Rozenski.

5.2 Mass Spectrometry is shared under a CC BY-NC-SA 4.0 license and was authored, remixed, and/or curated by LibreTexts.
Mass Spectrometry is licensed CC BY-NC-SA 4.0.

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5.3 Nuclear Magnetic Resonance (NMR) Spectroscopy
Introduction
Some types of atomic nuclei act as though they spin on their axis similar to the Earth. Since they are positively charged they
generate an electromagnetic field just as the Earth does. So, in effect, they will act as tiny bar magnetics. Not all nuclei act this way,
but fortunately both 1H and 13C do have nuclear spins and will respond to this technique.

NMR Spectrometer
In the absence of an external magnetic field the direction of the spin of the nuclei will be randomly oriented (see figure below left).
However, when a sample of these nuclei is place in an external magnetic field, the nuclear spins will adopt specific orientations
much as a compass needle responses to the Earth’s magnetic field and aligns with it. Two possible orientations are possible, with
the external field (i.e. parallel to and in the same direction as the external field) or against the field (i.e. antiparallel to the external
field). See figure below right.

Figure 1: (Left) Random nuclear spin without an external magnetic field. (Right)Ordered nuclear spin in an external magnetic field
If the ordered nuclei are now subjected to EM radiation of the proper frequency the nuclei aligned with the field will absorb energy
and "spin-flip" to align themselves against the field, a higher energy state. When this spin-flip occurs the nuclei are said to be in
"resonance" with the field, hence the name for the technique, Nuclear Magentic Resonance or NMR.
The amount of energy, and hence the exact frequency of EM radiation required for resonance to occur is dependent on both the
strength of the magnetic field applied and the type of the nuclei being studied. As the strength of the magnetic field increases the
energy difference between the two spin states increases and a higher frequency (more energy) EM radiation needs to be applied to
achieve a spin-flip (see image below).

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Superconducting magnets can be used to produce very strong magnetic field, on the order of 21 tesla (T). Lower field strengths can
also be used, in the range of 4 - 7 T. At these levels the energy required to bring the nuclei into resonance is in the MHz range and
corresponds to radio wavelength energies, i.e. at a field strength of 4.7 T 200 MHz bring 1H nuclei into resonance and 50 MHz
bring 13C into resonance. This is considerably less energy then is required for IR spectroscopy, ~10-4 kJ/mol versus ~5 - ~50
kJ/mol.
1H and 13C are not unique in their ability to undergo NMR. All nuclei with an odd number of protons (1H, 2H, 14N, 19F, 31P ...) or
nuclei with an odd number of neutrons (i.e. 13C) show the magnetic properties required for NMR. Only nuclei with even number of
both protons and neutrons (12C and 16O) do not have the required magnetic properties.
The basic arrangement of an NMR spectrometer is displayed below. A sample (in a small glass tube) is placed between the poles of
a strong magnetic. A radio frequency generator pulses the sample and excites the nuclei causing a spin-flip. The spin flip is
detected by the detector and the signal sent to a computer where it is processed.

Chemical Shifts
The NMR spectra is displayed as a plot of the applied radio frequency versus the absorption. The applied frequency increases from
left to right, thus the left side of the plot is the low field, downfield or deshielded side and the right side of the plot is the high field,
upfield or shielded side (see the figure below). The concept of shielding will be explained shortly.

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The position on the plot at which the nuclei absorbs is called the chemical shift. Since this has an arbitrary value a standard
reference point must be used. The two most common standards are TMS (tetramethylsilane, (Si(CH3)4) which has been assigned a
chemical shift of zero, and CDCl3 (deuterochloroform) which has a chemical shift of 7.26 for 1H NMR and 77 for 13C NMR.
The scale is commonly expressed as parts per million (ppm) which is independent of the spectrometer frequency. The scale is the
delta (δ) scale.

The range at which most NMR absorptions occur is quite narrow. Almost all 1H absorptions occur downfield within 10 ppm of
TMS. For 13C NMR almost all absorptions occurs within 220 ppm downfield of the C atom in TMS.

Shielding in NMR
Structural features of the molecule will have an effect on the exact magnitude of the magnetic field experienced by a particular
nucleus. This means that H atoms which have different chemical environments will have different chemical shifts. This is what
makes NMR so useful for structure determination in organic chemistry. There are three main features that will affect the shielding
of the nucleus, electronegativity, magnetic anisotropy of π systems and hydrogen bonding.

Electronegativity
The electrons that surround the nucleus are in motion so they created their own electromagnetic field. This field opposes the the
applied magnetic field and so reduces the field experienced by the nucleus. Thus the electrons are said to shield the nucleus. Since
the magnetic field experienced at the nucleus defines the energy difference between spin states it also defines what the chemical
shift will be for that nucleus. Electron with-drawing groups can decrease the electron density at the nucleus, deshielding the
nucleus and result in a larger chemical shift. Compare the data in the table below.

Compound,
CH3F CH3OH CH3Cl CH3Br CH3I CH4 (CH3)4Si
CH3X

Electronegativ
4.0 3.5 3.1 2.8 2.5 2.1 1.8
ity of X

Chemical shift
4.26 3.4 3.05 2.68 2.16 0.23 0
δ (ppm)

As can be seen from the data, as the electronegativity of X increases the chemical shift, δ increases. This is an effect of the halide
atom pulling the electron density away from the methyl group. This exposes the nuclei of both the C and H atoms, "deshielding"
the nuclei and shifting the peak downfield.
The effects are cumulative so the presence of more electron withdrawing groups will produce a greater deshielding and therefore a
larger chemical shift, i.e.

Compound CH4 CH3Cl CH2Cl2 CHCl3

δ (ppm) 0.23 3.05 5.30 7.27

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These inductive effects are not only felt by the immediately adjacent atoms, but the deshielding can occur further down the chain,
i.e.

NMR signal -CH2-CH2-CH2Br

δ (ppm) 1.25 1.69 3.30

Magnetic Anisotropy: π Electron Effects

The π electrons in a compound, when placed in a magnetic field, will move and generate their own magnetic field. The new
magnetic field will have an effect on the shielding of atoms within the field. The best example of this is benzene (see the figure
below).

This effect is common for any atoms near a π bond, i.e.

Proton Type Effect Chemical shift (ppm)

C6H5-H highly deshielded 6.5 - 8

C=C-H deshielded 4.5 - 6

C≡C-H shielded* ~2.5

O=C-H very highly deshielded 9 - 10

* the acetylene H is shielded due to its location relative to the π system

Hydrogen Bonding
Protons that are involved in hydrogen bonding (i.e.-OH or -NH) are usually observed over a wide range of chemical shifts. This is
due to the deshielding that occurs in the hydrogen bond. Since hydrogen bonds are dynamic, constantly forming, breaking and
forming again, there will be a wide range of hydrogen bonds strengths and consequently a wide range of deshielding. This as well
as solvation effects, acidity, concentration and temperature make it very difficult to predict the chemical shifts for these atoms.

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Experimentally -OH and -NH can be identified by carrying out a simple D2O exchange experiment since these protons are
exchangeable.
run the normal H-NMR experiment on your sample
add a few drops of D2O
re-run the H-NMR experiment
compare the two spectra and look for peaks that have "disappeared"

H-NMR Chemical Shifts

1H-NMR Spectra
1
An H-NMR will contain a unique signal for each different type of H atom present in the compound. What do we mean by "type"
of hydrogen atom? Since the amount of shielding is dependent on the local chemical environment, the exact chemical shift for H
atoms can vary widely. There are three basic methods you can use to determine if H atoms are identical.
1. Substitution method
This is the simplest but slowest method. The idea is to replace every H atom, one at a time with another atom i.e. a Cl atom to
see if you generate a different compound. Each different product indicates a different type of H atom.
2. Vebal Description
This requires to you describe each H atom verbally. If you have a different description then the H atoms are different.
For example:
An -NH is differnt from a -CH (based on the atom the H is attached to).
A -CH3 is different to a -CH2- (based on the number of attached hydrogen atoms).
An sp3 C-H is different than an sp2 C-H which is different to an sp C-H.
Others include position on a ring or chain, cis / trans relationships etc.
3. Symmetry
The symmetry method is the most sophisticated but requires a knowledge of molecular symmetry. H atoms that are related by
mirror planes, axis of rotation or a center of inversion are equivalent to one another.

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The first method is the easiet but slowest, the last is the fatest but requires a good knowledge of molecular symmetry. See the thre
examples below.
1
H-NMR Spectra: Intensity of Signals
There are several important pieces of information that you can obtain from an 1H-NMR. The first is the chemical shift of the peak.
This will aid in identifying the type of H atom that produced the signal. The second is the integration ratios of the peaks. The area
under a peak of a 1H-NMR is directly proportional to the number of H atoms that produced the peak. The area is calculated by
integrating the area, done automatically for you by the software. On older spectra the integration curve was drawn on the spectra,
modern software will produce this as a table attached to the spectra. The example below is for methyl t-butyl ether.

The integrals (shown as the red curves) are in a ratio of 333:1000 or 1:3. This implies that the peak on the left corresponds to the
methyl group attached to the oxygen (as expected since the O will deshield the H atoms). The peak on the right is the three methyl
groups of the t-butyl group, less deshielded as it is further away from the O atom. Note that we get the simplest ratio of H atom
types (1:3, methyl : t-butyl) not the true ratio of 3:9.

Spin-Spin Splitting
The NMR above has absorptions which are called singlets, a single sharp peak. However, in most cases, this is not the norm.
Absorptions are split into groups of peaks due to coupling between adjacent protons in the molecule.

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The 1H-NMR of 1,1,2-tribromoethane is shown above (integration ratios of 10:20 or 1:2). Note that the peaks are now split into a
group of two peaks on the right, a doublet and into three peaks on the left, a triplet. The relative areas under the peaks are 1:1 for
the doublet, and 1:2:1 for the triplet. The triplet corresponds to the -CHBr2 (most deshielded) proton and the doublet to the -CH2Br
(most shielded) protons. This also agrees with the integration.
Spin-spin splitting occurs between unique types of H atoms on the same or adjacent (vicinal) carbon atoms. This occurs because
the magnetic fields of each H atom can interact with the magnetic field of other H atoms. The interaction is only important (i.e.
leading to spin-spin splitting) when the H atoms are "chemically different" from one another (see preceding page).

Example: Splitting Patterns in 1,1,2-tribromoethane

The methine (-CH-) hydrogen can assume two magnetic spin orientations, with or against the external field. As a result the peak for the adjacent
methylene group is split into two lines of equal intensity, a doublet.

The methylene (-CH2-) hydrogen atoms can again assume one of two magnetic spin orientations, with or against the external field. However, in
this case these are two H atoms that are identical so there are three possible combinations of their two spins. The first (shown on the left) is both
are spin down, the next is both spin up (shown on the right). There are two possible ways for the 1 spin up and 1 spin down combination
depending on which specific H atom is spin up or down (shown in the center). The combination produces a triplet with relative intensities of
1:2:1 for the adjacent methine group.

Example: Splitting Patterns in bromoethane

The 1H-NMR for bromoethane is shown below (integration ratios of 20:30 or 2:3). Note the peaks are now split into a group of three peaks on the
right, a triplet and into four peaks on the left, a quartet. The relative areas under the peaks are 1:2:1 for the triplet and 1:3:3:1 for the quartet.
The quartet corresponds to the -CH2Br (most deshielded) protons and the triplet corresponds to the -CH3 most sheilded) protons. This also agrees
with the integration.

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 The methylene (-CH2-) hydrogen atoms can assume one of two magnetic spin orientations, with or against the external field. However, in this
case these are two H atoms that are identical so there are three possible combinations of their two spins. The first (shown on the left) is both are
spin down, the next is both spin up (shown on the right). There are two possible ways for the 1 spin up and 1 spin down combination depending
on which specific H atom is spin up or down (shown in the center). The combination produces a triplet with relative intensities of 1:2:1 for the
adjacent methyl group.

The methyl (-CH3) hydrogen atoms can again assume one of two magnetic spin orientations, with or against the external field. However in this
case there are three protons that are identical so there are four possible combinations of their spins. The most deshielded peak will occur when all
three spins are aligned with the field (left most image). The most shielded peak occurs when all three spins are aligned against the field (the right
most image). There are now two possibilities left, the case where two spins are with and one against field or two spins against and one with the
field. The first case will be mose deshielded than the second case and so downfield form it. This combination will split the adjacent peak for the
methylene protons into a quartet with relative intensities of 1:3:3:1.

Coupling Constant, J

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The coupling constant, (symbol J, units Hz) is a measure of the interaction between a pair of protons.
In a vicinal type of system, Ha-C-C-Hb the coupling between protons Ha and Hb is Jab. The coupling of Hb and Ha must be equal
to the coupling between Ha and Hb, of Jab = Jba.
The implications of this is that the spacing betwen the lines for peaks that are coupled must be the same. Compare the peaks from
1,1,2-tribromoethane shown right. This means we can identify which peaks are coupled by the spacing between the lines.

Common Spin Multiplicities

Number of equivalent
Multiplicity Ratio of Intensities
adjacent protons

0 singlet 1

1 doublet 1:1

2 triplet 1:2:1

3 quartet 1:3:3:1

4 quintet 1:4:6:4:1

5 hextet 1:5:10:10:5:1

6 septet 1:6:15:20:15:6:1

Summary
First, the chemical shift or location of the peak (in ppm) tells you how deshielded the protons are and hence their "local
chemical environment", i.e. what possible deshielding groups maybe adjacent to the protons.
Second, the integration ratios tell you the number of each type of proton in the simplest ratio.
Third, the spin-spin splitting (coupling pattern or multiplicity) tells you the number of protons on the adjacent C atom. It will be
one less than the number of peaks.
This information combined gives us the basic skeletal structure of the molecule.

Sample 1H-NMR Spectra

List of Animated 1H-NMR Spectra

1- 3-
Bromoeth 2-
bromopro bromopro propanal
ane propanol
pane pene

2-
propanoic ethyl
Phenol acetone propenam
acid acetate
ide
For all spectra click on a peak to highlight the protons
responsible for the peak.
More spectra can be found at Animated Spectra

To see the integratals, right click on the spectra to open the menu, go to "view" and check the integrate" box.

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Contributors
Dr. Richard Spinney (The Ohio State University)

5.3 Nuclear Magnetic Resonance (NMR) Spectroscopy is shared under a CC BY-NC-SA 4.0 license and was authored, remixed, and/or curated by
LibreTexts.

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5.4 Ultraviolet (UV) Spectroscopy
1. Contributors
A diagram of the components of a typical spectrometer are shown in the following diagram. The functioning of this instrument is
relatively straightforward. A beam of light from a visible and/or UV light source (colored red) is separated into its component
wavelengths by a prism or diffraction grating. Each monochromatic (single wavelength) beam in turn is split into two equal
intensity beams by a half-mirrored device. One beam, the sample beam (colored magenta), passes through a small transparent
container (cuvette) containing a solution of the compound being studied in a transparent solvent. The other beam, the reference
(colored blue), passes through an identical cuvette containing only the solvent. The intensities of these light beams are then
measured by electronic detectors and compared. The intensity of the reference beam, which should have suffered little or no light
absorption, is defined as I0. The intensity of the sample beam is defined as I. Over a short period of time, the spectrometer
automatically scans all the component wavelengths in the manner described. The ultraviolet (UV) region scanned is normally from
200 to 400 nm, and the visible portion is from 400 to 800 nm.

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 If the sample compound does not absorb light
of of a given wavelength, I = I0. However, if
the sample compound absorbs light then I is
less than I0, and this difference may be plotted
on a graph versus wavelength, as shown on the
right. Absorption may be presented as
transmittance (T = I/I0) or absorbance (A=
log I0/I). If no absorption has occurred, T =
1.0 and A= 0. Most spectrometers display
absorbance on the vertical axis, and the
commonly observed range is from 0 (100%
transmittance) to 2 (1% transmittance). The
wavelength of maximum absorbance is a
characteristic value, designated as λmax.
Different compounds may have very different
absorption maxima and absorbances. Intensely
absorbing compounds must be examined in
dilute solution, so that significant light energy
is received by the detector, and this requires
the use of completely transparent (non-
absorbing) solvents. The most commonly used
solvents are water, ethanol, hexane and
cyclohexane. Solvents having double or triple
bonds, or heavy atoms (e.g. S, Br & I) are
generally avoided. Because the absorbance of
a sample will be proportional to its molar
concentration in the sample cuvette, a
corrected absorption value known as the
molar absorptivity is used when comparing
the spectra of different compounds. This is
defined as:
( where A= absorbance,
c = sample
concentration in
Molar Absorptivity
moles/liter
ε = A/ c l
& l = length of light
path through the cuvette
in cm.)

For the spectrum on the right, a solution of 0.249 mg of the unsaturated aldehyde in 95% ethanol (1.42 • 10-5 M) was placed in a 1
cm cuvette for measuement. Using the above formula, ε = 36,600 for the 395 nm peak, and 14,000 for the 255 nm peak. Note that
the absorption extends into the visible region of the spectrum, so it is not surprising that this compound is orange colored.
Molar absoptivities may be very large for strongly absorbing compounds (ε >10,000) and very small if absorption is weak (ε
= 10 to 100).

Contributors
William Reusch, Professor Emeritus (Michigan State U.), Virtual Textbook of Organic Chemistry

5.4 Ultraviolet (UV) Spectroscopy is shared under a CC BY-NC-SA 4.0 license and was authored, remixed, and/or curated by LibreTexts.

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5.5 Polarimetry
 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 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
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.

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 6 8
4
2 7

1
Figure 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:
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

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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 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.
ee = [(% more abundant enantiomer – 50) × 100]/50. = [68.9 – 50) × 100]/50 = 37.8%.

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 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 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 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 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
b. cholesterol ([α]D = - 31.5) levorotatory
c. cocaine ([α]D = - 16) levorotatory

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 d. chloroform ([α]D = 0) neither, not optically active

 Exercise 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 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 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 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 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

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  Exercise 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 6d

Determine the ee’s of the following from the percentages

50 % (S) alanine

Answer
(50 – 50) x 100] / 50 = 0 % ee, racemic mixture

5.5 Polarimetry is shared under a CC BY-NC-SA 4.0 license and was authored, remixed, and/or curated by LibreTexts.
5.3: Optical Activity by Dietmar Kennepohl, Krista Cunningham, Steven Farmer, Tim Soderberg, Zachary Sharrett is licensed CC BY-SA
4.0.

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 CHAPTER OVERVIEW

Chapter 6. Reactive Intermediates

Purdue CHM 26505: Organic

Chemistry for Chemistry Majors (1st
Semester)
Fall 2014: Prof. Mark Lipton

Template:HideTOC

Topic hierarchy
6.1 Carbocations
6.2: Carbanions
6.3 Free Radicals

Chapter 6. Reactive Intermediates is shared under a CC BY-NC-SA 4.0 license and was authored, remixed, and/or curated by LibreTexts.

1
6.1 Carbocations
A carbocation is an ion with a positively-charged carbon atom. Among the simplest examples are methenium CH3+, methanium
CH5+, and ethanium C2H7+. Some carbocations may have two or more positive charges, on the same carbon atom or on different
atoms; such as the ethylene dication C2H42+.[1]

Definitions
Until the early 1970s, all carbocations were called carbonium ions.[2] In present-day chemistry, a carbocation is any positively
charged carbon atom, classified in two main categories according to the valence of the charged carbon:
+3 in carbenium ions (protonated carbenes),
+5 or +6 in the carbonium ions (protonated alkanes, named by analogy to ammonium).
This nomenclature was proposed by G. A. Olah.[3] University-level textbooks discuss carbocations only as if they are carbenium
ions,[4] or discuss carbocations with a fleeting reference to the older phrase of carbonium ion[5] or carbenium and carbonium ions.
[6]

History
The history of carbocations dates back to 1891 when G. Merling[8] reported that he added bromine to tropylidene
(cycloheptatriene) and then heated the product to obtain a crystalline, water-soluble material, C H Br. He did not suggest a
7 7

structure for it; however, Doering and Knox[9] convincingly showed that it was tropylium (cycloheptatrienylium) bromide. This
ion is predicted to be aromatic by Hückel's rule.
In 1902, Norris and Kehrman independently discovered that colorless triphenylmethanol gives deep-yellow solutions in
concentrated sulfuric acid. Triphenylmethyl chloride similarly formed orange complexes with aluminium and tin chlorides. In
1902, Adolf von Baeyer recognized the salt-like character of the compounds formed.

He dubbed the relationship between color and salt formation halochromy, of which malachite green is a prime example.
Carbocations are reactive intermediates in many organic reactions. This idea, first proposed by Julius Stieglitz in 1899,[10] was
further developed by Hans Meerwein in his 1922 study[11][12] of the Wagner-Meerwein rearrangement. Carbocations were also
found to be involved in the S 1 reaction, the \(E1\0 reaction, and in rearrangement reactions such as the Whitmore 1,2 shift. The
N

chemical establishment was reluctant to accept the notion of a carbocation and for a long time the Journal of the American
Chemical Society refused articles that mentioned them.
The first NMR spectrum of a stable carbocation in solution was published by Doering et al.[13] in 1958. It was the
heptamethylbenzenium ion, made by treating hexamethylbenzene with methyl chloride and aluminium chloride. The stable 7-
norbornadienyl cation was prepared by Story et al. in 1960[14] by reacting norbornadienyl chloride with silver tetrafluoroborate in
sulfur dioxide at −80 °C. The NMR spectrum established that it was non-classically bridged (the first stable non-classical ion
observed).
In 1962, Olah directly observed the tert-butyl carbocation by nuclear magnetic resonance as a stable species on dissolving tert-butyl
fluoride in magic acid. The NMR of the norbornyl cation was first reported by Schleyer et al.[15] and it was shown to undergo
proton-scrambling over a barrier by Saunders et al.[16]

Structure and properties

The charged carbon atom in a carbocation is a "sextet", i.e. it has only six electrons in its outer valence shell instead of the eight
valence electrons that ensures maximum stability (octet rule). Therefore, carbocations are often reactive, seeking to fill the octet of
valence electrons as well as regain a neutral charge. One could reasonably assume a carbocation to have sp hybridization with an
3

1 https://chem.libretexts.org/@go/page/17125
empty sp orbital giving positive charge. However, the reactivity of a carbocation more closely resembles
3 sp
2
hybridization with
atrigonal planar molecular geometry. An example is the methyl cation, C H . 3
+

Order of stability of examples of tertiary (III), secondary (II), and primary (I) alkylcarbenium ions, as well as the methyl cation (far
right).
Carbocations are often the target of nucleophilic attack by nucleophiles like hydroxide (OH−) ions or halogen ions.
Carbocations typically undergo rearrangement reactions from less stable structures to equally stable or more stable ones with rate
constants in excess of 109/sec. This fact complicates synthetic pathways to many compounds. For example, when 3-pentanol is
heated with aqueous HCl, the initially formed 3-pentyl carbocation rearranges to a statistical mixture of the 3-pentyl and 2-pentyl.
These cations react with chloride ion to produce about 1/3 3-chloropentane and 2/3 2-chloropentane.
A carbocation may be stabilized by resonance by a carbon-carbon double bond next to the ionized carbon. Such cations as allyl
cation CH2=CH–CH2+ and benzyl cation C6H5–CH2+ are more stable than most other carbocations. Molecules that can form allyl
or benzyl carbocations are especially reactive. These carbocations where the C+ is adjacent to another carbon atom that has a
double or triple bond have extra stability because of the overlap of the empty p orbital of the carbocation with the p orbitals of the π
bond. This overlap of the orbitals allows the charge to be shared between multiple atoms – delocalization of the charge - and,
therefore, stabilizes the carbocation.

Non-classical ions
Some carbocations such as the norbornyl cation exhibit more or less symmetrical three centre bonding. Cations of this sort have
been referred to as non-classical ions. The energy difference between "classical" carbocations and "non-classical" isomers is often
very small, and in general there is little, if any, activation energy involved in the transition between "classical" and "non-classical"
structures. In essence, the "non-classical" form of the 2-butyl carbocation is 2-butene with a proton directly above the centre of
what would be the carbon-carbon double bond. "Non-classical" carbocations were once the subject of great controversy. One of
George Olah's greatest contributions to chemistry was resolving this controversy.[17]

Specific carbocations
Cyclopropylcarbinyl cations can be studied by NMR:[18][19]

In the NMR spectrum of a dimethyl derivative, two nonequivalent signals are found for the two methyl groups, indicating that the
molecular conformation of this cation not perpendicular (as in A) but is bisected (as in B) with the empty p-orbital and the
cyclopropyl ring system in the same plane:

In terms of bent bond theory, this preference is explained by assuming favorable orbital overlap between the filled cyclopropane
bent bonds and the empty p-orbital.[20]

References
1. Hansjörg Grützmacher, Christina M. Marchand (1997), "Heteroatom stabilized carbenium ions", Coordination Chemistry
Reviews, volume 163, pages 287-344. doi:10.1016/S0010-8545(97)00043-X

2 https://chem.libretexts.org/@go/page/17125
 2. Gold Book definition carbonium ion HTML
3. George A. Olah (1972), "Stable carbocations. CXVIII. General concept and structure of carbocations based on differentiation of
trivalent (classical) carbenium ions from three-center bound penta- of tetracoordinated (nonclassical) carbonium ions. Role of
carbocations in electrophilic reactions." Journal of the American Chemical Society, volume 94, issue 3, pages 808–820
doi:10.1021/ja00758a020
4. Organic chemistry 5th Ed. John McMurry ISBN 0-534-37617-7
5. Organic Chemistry, Fourth Edition Paula Yurkanis Bruice ISBN 0-13-140748-1
6. Clayden, Jonathan; Greeves, Nick; Warren, Stuart; Wothers, Peter (2001). Organic Chemistry (1st ed.). Oxford University
Press. ISBN 978-0-19-850346-0.
7. Organic Chemistry by Marye Anne Fox and James K. Whitesell ISBN 0-7637-0413-X
8. Chem. Ber. 24, 3108 1891
9. The Cycloheptatrienylium (Tropylium) Ion W. Von E. Doering and L. H. Knox J. Am. Chem. Soc.; 1954; 76(12) pp 3203 -
3206; doi:10.1021/ja01641a027
10. On the Constitution of the Salts of Imido-Ethers and other Carbimide Derivatives; Am. Chem. J. 21, 101; ISSN: 0096-4085
11. H. Meerwein and K. van Emster, Berichte, 1922, 55, 2500.
12. Rzepa, H. S.; Allan, C. S. M. (2010). "Racemization of Isobornyl Chloride via Carbocations: A Nonclassical Look at a Classic
Mechanism". Journal of Chemical Education 87 (2): 221. Bibcode:2010JChEd..87..221R. doi:10.1021/ed800058c. edit
13. The 1,1,2,3,4,5,6-heptamethylbenzenonium ion W. von E. Doering and M. Saunders H. G. Boyton, H. W. Earhart, E. F. Wadley
and W. R. Edwards G. Laber Tetrahedron Volume 4, Issues 1-2 , 1958, Pages 178-185 doi:10.1016/0040-4020(58)88016-3
14. The 7-norbornadienyl carbonium ion Paul R. Story and Martin Saunders J. Am. Chem. Soc.; 1960; 82(23) pp 6199 - 6199;
doi:10.1021/ja01508a058
15. Stable Carbonium Ions. X.1 Direct Nuclear Magnetic Resonance Observation of the 2-Norbornyl Cation Paul von R. Schleyer,
William E. Watts, Raymond C. Fort, Melvin B. Comisarow, and George A. Olah J. Am. Chem. Soc.; 1964; 86(24) pp 5679 -
5680; doi:10.1021/ja01078a056
16. Stable Carbonium Ions. XI.1 The Rate of Hydride Shifts in the 2-Norbornyl Cation Martin Saunders, Paul von R. Schleyer, and
George A. Olah J. Am. Chem. Soc.; 1964; 86(24) pp 5680 - 5681; doi:10.1021/ja01078a057
17. George A. Olah - Nobel Lecture
18. Nuclear magnetic double resonance studies of the dimethylcyclopropylcarbinyl cation. Measurement of the rotation barrier
David S. Kabakoff, , Eli. Namanworth J. Am. Chem. Soc. 1970, 92 (10), pp 3234–3235 doi:10.1021/ja00713a080
19. Stable Carbonium Ions. XVII.1a Cyclopropyl Carbonium Ions and Protonated Cyclopropyl Ketones Charles U. Pittman Jr.,
George A. Olah J. Am. Chem. Soc., 1965, 87 (22), pp 5123–5132 doi:10.1021/ja00950a026
20. F.A. Carey, R.J. Sundberg Advanced Organic Chemistry Part A 2nd Ed.

6.1 Carbocations is shared under a CC BY-NC-SA 4.0 license and was authored, remixed, and/or curated by LibreTexts.
Carbocations is licensed CC BY-NC-SA 4.0.

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6.2: Carbanions
A carbanion is an anion in which carbon has an unshared pair of electrons and bears a negative charge usually with three substituents for a total of eight valence electrons.[1] The
carbanion exists in a trigonal pyramidal geometry. Formally, a carbanion is the conjugate base of a carbon acid.
− −
R C−H + B → R C + H−B (6.2.1)
3 3

where B stands for the base. A carbanion is one of several reactive intermediates in organic chemistry.

Theory
A carbanion is a nucleophile, which stability and reactivity determined by several factors:
1. The inductive effect. Electronegative atoms adjacent to the charge will stabilize the charge;
2. Hybridization of the charge-bearing atom. The greater the s-character of the charge-bearing atom, the more stable the anion;
3. The extent of conjugation of the anion. Resonance effects can stabilize the anion. This is especially true when the anion is stabilized as a result of aromaticity.
A carbanion is a reactive intermediate and is encountered in organic chemistry for instance in the E1cB elimination reaction and in organometallic chemistry in for instance a Grignard
reaction or in alkyl lithium chemistry. Stable carbanions do however exist. In 1984 Olmstead presented the lithium crown ether salt of the triphenylmethyl carbanion from
triphenylmethane, n-butyllithium and 12-crown-4 at low temperatures:[2]

Adding n-butyllithium to triphenylmethane in THF at low temperatures followed by 12-crown-4 results in a red solution and the salt complex precipitates at −20 °C. The central C-C
bond lengths are 145 pm with the phenyl ring propelled at an average angle of 31.2°. This propeller shape is less pronounced with a tetramethylammonium counterion.[3] One tool for
the detection of carbanions in solution is proton NMR.[4] A spectrum of cyclopentadiene in DMSO shows four vinylic protons at 6.5 ppm and two methylene bridge protons at 3 ppm
whereas the cyclopentadienyl anion has a single resonance at 5.50 ppm.

Carbon acids
Any molecule containing a C-H can lose a proton forming the carbanion. Hence any hydrocarbon containing C-H bonds can be considered an acid with a corresponding pKa value.
Methane is certainly not an acid in its classical meaning yet its estimated pKa is 56. Compare this to acetic acid with pKa 4.76. The same factors that determine the stability of the
carbanion also determine the order in pKa in carbon acids. These values are determined for the compounds either in water in order to compare them to ordinary acids, indimethyl
sulfoxide in which the majority of carbon acids and their anions are soluble or in the gas phase. With DMSO the acidity window for solutes is limited to its own pKa of 35.5.
Table 1. Carbon acid acidities in pKa in DMSO [5]. Reference acids in bold.
name formula structural formula pKa

Methane CH4 Methane-2D-dimensions.svg ~ 56

Ethane C2H6 Ethane-staggered-CRC-MW-dimensions-2D.png ~ 50

Anisole C7H8O Anisol.svg ~ 49

Cyclopentane C5H10 Cyclopentane2d.png ~ 45

Propene C3H6 Propylene skeletal.svg ~ 44

Benzene C6H6 Benzol.svg ~ 43

Toluene C6H5CH3 Toluol.svg ~ 43

Dimethyl sulfoxide (CH3)2SO DMSO-2D-dimensions.png 35.5

Diphenylmethane C13H12 Diphenylmethane.png 32.3

Aniline C6H5NH2 Aniline.svg 30.6

Triphenylmethane C19H16 Triphenylmethane.png 30.6

Xanthene C13H10O Xanthen.svg 30

Ethanol C2H5OH Ethanol-2D-skeletal.svg 29.8

Phenylacetylene C8H6 Phenylacetylene.svg 28.8

Thioxanthene C13H10S Thioxanthene.png 28.6

Acetone C3H6O Aceton.svg 26.5

Acetylene C2H2 Acetylene-CRC-IR-dimensions-2D.png 25

Benzoxazole C7H5NO 1,3-benzoxazole numbering.svg 24.4

Fluorene C13H10 Fluorene.png 22.6

Indene C9H8 Indene.png 20.1

Cyclopentadiene C5H6 Cyclopentadiene.png 18

Malononitrile C3H2N2 Malononitrile.png 11.2

Hydrogen cyanide HCN Hydrogen-cyanide-2D.svg 9.2

Acetylacetone C5H8O2 AcacH.png 8.95

Dimedone C8H12O2 Dimedone.png 5.23

Meldrum's acid C6H8O4 Meldrum's acid.png 4.97

Acetic acid CH3COOH Acetic-acid-2D-skeletal.svg 4.76

6.2.1 https://chem.libretexts.org/@go/page/17126
 name formula structural formula pKa

Barbituric acid C4H2O3(NH)2 Barbituric acid.png 4.01

Trinitromethane HC(NO2)3 Trinitromethane.svg 0.17

Fulminic acid HCNO Fulminsäure.png -1.07

Carborane superacid HCHB11Cl11 Carborane-acid-3D-balls.png -9

Note that the anions formed by ionization of acetic acid, ethanol or aniline are not carbanions.

Starting from methane in Table 1, the acidity increases:

when the anion is aromatic, either because the added electron causes the anion to become aromatic (as in indene and cyclopentadiene), or because the negative charge on carbon can
be delocalized over several already-aromatic rings (as in triphenylmethane or the carborane superacid).
when the carbanion is surrounded by strongly electronegative groups, through the partial neutralisation of the negative charge (as in malononitrile).
when the carbanion is immediately next to a carbonyl group. The α-protons of carbonyl groups are acidic because the negative charge in the enolate can be partially distributed in the
oxygen atom. Meldrum's acid and barbituric acid, historically named acids, are in fact a lactone and a lactam respectively, but their acidic carbon protons make them acidic. The
acidity of carbonyl compounds is an important driving force in many organic reactions such as the aldol reaction.

Chiral carbanions
With the molecular geometry for a carbanion described as a trigonal pyramid the question is whether or not carbanions can display chirality, because if the activation barrier for
inversion of this geometry is too low any attempt at introducing chirality will end inracemization, similar to the nitrogen inversion. However, solid evidence exists that carbanions can
indeed be chiral for example in research carried out with certain organolithium compounds.
The first ever evidence for the existence of chiral organolithium compounds was obtained in 1950. Reaction of chiral 2-iodooctane with sec-butyllithium in petroleum ether at −70 °C
followed by reaction with dry ice yielded mostly racemic 2-methylbutyric acid but also an amount of optically active 2-methyloctanoic acid which could only have formed from
likewise optical active 2-methylheptyllithium with the carbon atom linked to lithium the carbanion:[6]

On heating the reaction to 0 °C the optical activity is lost. More evidence followed in the 1960s. A reaction of the cis isomer of 2-methylcyclopropyl bromide with sec-butyllithium
again followed by carboxylation with dry ice yielded cis-2-methylcyclopropylcarboxylic acid. The formation of the trans isomer would have indicated that the intermediate carbanion
was unstable.[7]

In the same manner the reaction of (+)-(S)-l-bromo-l-methyl-2,2-diphenylcyclopropane with n-butyllithium followed by quench with methanol resulted in product with retention of
configuration:[8]

Of recent date are chiral methyllithium compounds:[9]

The phosphate 1 contains a chiral group with a hydrogen and a deuterium substituent. The stannyl group is replaced by lithium to intermediate 2 which undergoes a phosphate-
phosphorane rearrangement to phosphorane 3 which on reaction with acetic acid givesalcohol 4. Once again in the range of −78 °C to 0 °C the chirality is preserved in this reaction
sequence.[10]

 History

A carbanionic structure first made an appearance in the reaction mechanism for the benzoin condensation as correctly proposed by Clarke and Lapworth in 1907.[11] In 1904
Schlenk prepared Ph3C-NMe4+ in a quest for pentavalent nitrogen (fromTetramethylammonium chloride and Ph3CNa) [12] and in 1914 he demonstrated how triarylmethyl radicals
could be reduced to carbonions by alkali metals.[13] The phrase carbanion was introduced by Wallis and Adams in 1933 as the negatively charged counterpart of the carbonium ion.
[14][15]

6.2.2 https://chem.libretexts.org/@go/page/17126
External links
Large database of Bordwell pKa values at www.chem.wisc.edu Link
Large database of Bordwell pKa values at daecr1.harvard.edu Link

References
1. Organic Chemistry - Robert Thornton Morrison, Robert Neilson Boyd
2. The isolation and x-ray structures of lithium crown ether salts of the free phenyl carbanions [CHPh2]- and [CPh3]- Marilyn M. Olmstead, Philip P. Power; J. Am. Chem. Soc.;
1985; 107(7); 2174-2175. doi:10.1021/ja00293a059
3. Harder, Sjoerd (2002). "Schlenk's Early “Free” Carbanions". Chemistry - A European Journal 8 (14): 3229–3232. doi:10.1002/1521-3765(20020715)8:14<3229::AID-
CHEM3229>3.0.CO;2-3.
4. A Simple and Convenient Method for Generation and NMR Observation of Stable Carbanions. Hamid S. Kasmai Journal of Chemical Education • Vol. 76 No. 6 June 1999
5. Equilibrium acidities in dimethyl sulfoxide solution Frederick G. Bordwell Acc. Chem. Res.; 1988; 21(12) pp 456 - 463; doi:10.1021/ar00156a004
6. FORMATION OF OPTICALLY ACTIVE 1-METHYLHEPTYLLITHIUM Robert L. Letsinger J. Am. Chem. Soc.; 1950; 72(10) pp 4842 - 4842; doi:10.1021/ja01166a538
7. The Configurational Stability of cis- and trans-2-Methylcyclopropyllithium and Some Observations on the Stereochemistry of their Reactions with Bromine and Carbon Dioxide
Douglas E. Applequist and Alan H. Peterson J. Am. Chem. Soc.; 1961; 83(4) pp 862 - 865;doi:10.1021/ja01465a030
8. Cyclopropanes. XV. The Optical Stability of 1-Methyl-2,2-diphenylcyclopropyllithium H. M. Walborsky, F. J. Impastato, and A. E. Young J. Am. Chem. Soc.; 1964; 86(16) pp 3283 -
3288; doi:10.1021/ja01070a017
9. Preparation of Chiral -Oxy-[2H1]methyllithiums of 99% ee and Determination of Their Configurational Stability Dagmar Kapeller, Roland Barth, Kurt Mereiter, and Friedrich
Hammerschmidt J. Am. Chem. Soc.; 2007; 129(4) pp 914 - 923; (Article) doi:10.1021/ja066183s
10. Enantioselectivity determined by NMR spectroscopy after derivatization with Mosher's acid
11. Clarke, R. W. L.; Lapworth, A. (1907). "LXV.?An extension of the benzoin synthesis". Journal of the Chemical Society, Transactions 91: 694. doi:10.1039/CT9079100694.
12. Schlenk, W.; Weickel, T.; Herzenstein, A. (1910). "Ueber Triphenylmethyl und Analoga des Triphenylmethyls in der Biphenylreihe. [Zweite Mittheilung über „Triarylmethyle”.]".
Justus Liebig's Annalen der Chemie 372: 1. doi:10.1002/jlac.19103720102.
13. Schlenk, W.; Marcus, E. (1914). "Über Metalladditinen an freie organische Radikale. (Über Triarylmethyle. XII.)". Berichte der deutschen chemischen Gesellschaft 47 (2): 1664.
doi:10.1002/cber.19140470256.
14. Wallis, E. S.; Adams, F. H. (1933). "The Spatial Configuration of the Valences in Tricovalent Carbon Compounds1". Journal of the American Chemical Society 55 (9): 3838.
doi:10.1021/ja01336a068.
15. Tidwell, T. T. (1997). "The first century of physical organic chemistry: A prologue". Pure and Applied Chemistry 69 (2): 211–214. doi:10.1351/pac199769020211. edi

6.2: Carbanions is shared under a CC BY-NC-SA 4.0 license and was authored, remixed, and/or curated by LibreTexts.
Carbanions II is licensed CC BY-NC-SA 4.0.

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6.3 Free Radicals
In chemistry, a radical (more precisely, a free radical) is an atom, molecule, or ion that has unpaired valence electrons or an open electron shell, and therefore may be seen as having
one or more "dangling" covalent bonds.
With some exceptions, these "dangling" bonds make free radicals highly chemically reactive towards other substances, or even towards themselves: their molecules will often
spontaneously dimerize or polymerize if they come in contact with each other. Most radicals are reasonably stable only at very low concentrations in inert media or in a vacuum.
A notable example of a free radical is the hydroxyl radical (HO•), a molecule that is one hydrogen atom short of a water molecule and thus has one bond "dangling" from the oxygen.
Two other examples are the carbene molecule (:CH2), which has two dangling bonds; and the superoxide anion (•O−2), the oxygen molecule O2 with one extra electron, which has one
dangling bond. In contrast, the hydroxyl anion (HO−), the oxide anion (O2−) and thecarbenium cation (CH+3) are not radicals, since the bonds that may appear to be dangling are in fact
resolved by the addition or removal of electrons.
Free radicals may be created in a number of ways, including synthesis with very dilute or rarefied reagents, reactions at very low temperatures, or breakup of larger molecules. The latter
can be affected by any process that puts enough energy into the parent molecule, such as ionizing radiation, heat, electrical discharges, electrolysis, and chemical reactions. Indeed,
radicals are intermediate stages in many chemical reactions.
Free radicals play an important role in combustion, atmospheric chemistry, polymerization, plasma chemistry, biochemistry, and many other chemical processes. In living organisms, the
free radicals superoxide and nitric oxideand their reaction products regulate many processes, such as control of vascular tone and thus blood pressure. They also play a key role in the
intermediary metabolism of various biological compounds. Such radicals can even be messengers in a process dubbed redox signaling. A radical may be trapped within a solvent cage or
be otherwise bound.
Until late in the 20th century the word "radical" was used in chemistry to indicate any connected group of atoms, such as a methyl group or a carboxyl, whether it was part of a larger
molecule or a molecule on its own. The qualifier "free" was then needed to specify the unbound case. Following recent nomenclature revisions, a part of a larger molecule is now called
a functional group or substituent, and "radical" now implies "free". However, the old nomenclature may still occur in the literature.

History
The first organic free radical identified was triphenylmethyl radical. This species was discovered by Moses Gomberg in 1900 at the University of Michigan USA. Historically, the term
radical in radical theory was also used for bound parts of the molecule, especially when they remain unchanged in reactions. These are now called functional groups. For example,
methyl alcohol was described as consisting of a methyl "radical" and a hydroxyl "radical". Neither are radicals in the modern chemical sense, as they are permanently bound to each
other, and have no unpaired, reactive electrons; however, they can be observed as radicals in mass spectrometry when broken apart by irradiation with energetic electrons.

Depiction in chemical reactions

In chemical equations, free radicals are frequently denoted by a dot placed immediately to the right of the atomic symbol or molecular formula as follows:

Chlorine gas can be broken down by ultraviolet light to form atomic chlorine radicals.

Radical reaction mechanisms use single-headed arrows to depict the movement of single electrons:
Radical.svg

The homolytic cleavage of the breaking bond is drawn with a 'fish-hook' arrow to distinguish from the usual movement of two electrons depicted by a standard curly arrow. It should be
noted that the second electron of the breaking bond also moves to pair up with the attacking radical electron; this is not explicitly indicated in this case.
Free radicals also take part in radical addition and radical substitution as reactive intermediates. Chain reactions involving free radicals can usually be divided into three distinct
processes. These are initiation, propagation, and termination.
Initiation reactions are those that result in a net increase in the number of free radicals. They may involve the formation of free radicals from stable species as in Reaction 1 above or
they may involve reactions of free radicals with stable species to form more free radicals.
Propagation reactions are those reactions involving free radicals in which the total number of free radicals remains the same.
Termination reactions are those reactions resulting in a net decrease in the number of free radicals. Typically two free radicals combine to form a more stable species, for example:
2Cl·→ Cl2

Formation
The formation of radicals may involve breaking of covalent bonds homolytically, a process that requires significant amounts of energy. For example, splitting H2 into 2H· has a ΔH° of
+435 kJ/mol, and Cl2 into 2Cl· has a ΔH° of +243 kJ/mol. This is known as the homolytic bond dissociation energy, and is usually abbreviated as the symbol ΔH°. The bond energy
between two covalently bonded atoms is affected by the structure of the molecule as a whole, not just the identity of the two atoms. Likewise, radicals requiring more energy to form are
less stable than those requiring less energy. Homolytic bond cleavage most often happens between two atoms of similar electronegativity. In organic chemistry this is often the O-O bond
in peroxide species or O-N bonds. Sometimes radical formation is spin-forbidden, presenting an additional barrier. However, propagation is a very exothermic reaction. Likewise,
although radical ions do exist, most species are electrically neutral. Radicals may also be formed by single electron oxidation or reduction of an atom or molecule. An example is the
production of superoxide by the electron transport chain. Early studies of organometallic chemistry, especially tetra-alkyl lead species by F.A. Paneth and K. Hahnfeld in the 1930s
supported heterolytic fission of bonds and a radical based mechanism.

Persistence and stability

The radical derived from α-tocopherol

Although radicals are generally short-lived due to their reactivity, there are long-lived radicals. These are categorized as follows:

Stable radicals

The prime example of a stable radical is molecular dioxygen (O2). Another common example is nitric oxide (NO). Organic radicals can be long lived if they occur in a conjugated π
system, such as the radical derived from α-tocopherol (vitamin E). There are also hundreds of examples of thiazyl radicals, which show low reactivity and remarkable thermodynamic
stability with only a very limited extent of π resonance stabilization.[1][2]

Persistent radicals

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Persistent radical compounds are those whose longevity is due to steric crowding around the radical center, which makes it physically difficult for the radical to react with another
molecule.[3] Examples of these include Gomberg's triphenylmethyl radical, Fremy's salt(Potassium nitrosodisulfonate, (KSO3)2NO·), nitroxides, (general formula R2NO·) such as
TEMPO, TEMPOL, nitronyl nitroxides, and azephenylenyls and radicals derived from PTM (perchlorophenylmethyl radical) and TTM (tris(2,4,6-trichlorophenyl)methyl radical).
Persistent radicals are generated in great quantity during combustion, and "may be responsible for the oxidative stress resulting in cardiopulmonary disease and probably cancer that has
been attributed to exposure to airborne fine particles."[4]

Diradicals

Diradicals are molecules containing two radical centers. Multiple radical centers can exist in a molecule. Atmospheric oxygen naturally exists as a diradical in its ground state as triplet
oxygen. The low reactivity of atmospheric oxygen is due to its diradical state. Non-radical states of dioxygen are actually less stable than the diradical. The relative stability of the
oxygen diradical is primarily due to the spin-forbidden nature of the triplet-singlet transition required for it to grab electrons, i.e., "oxidize". The diradical state of oxygen also results in
its paramagnetic character, which is demonstrated by its attraction to an external magnet.[5]

Reactivity
Radical alkyl intermediates are stabilized by similar physical processes to carbocations: as a general rule, the more substituted the radical center is, the more stable it is. This directs their
reactions. Thus, formation of a tertiary radical (R3C·) is favored over secondary (R2HC·), which is favored over primary (RH2C·). Likewise, radicals next to functional groups such as
carbonyl, nitrile, and ether are more stable than tertiary alkyl radicals.
Radicals attack double bonds. However, unlike similar ions, such radical reactions are not as much directed by electrostatic interactions. For example, the reactivity of nucleophilic ions
with α,β-unsaturated compounds (C=C–C=O) is directed by the electron-withdrawing effect of the oxygen, resulting in a partial positive charge on the carbonyl carbon. There are two
reactions that are observed in the ionic case: the carbonyl is attacked in a direct addition to carbonyl, or the vinyl is attacked in conjugate addition, and in either case, the charge on the
nucleophile is taken by the oxygen. Radicals add rapidly to the double bond, and the resulting α-radical carbonyl is relatively stable; it can couple with another molecule or be oxidized.
Nonetheless, the electrophilic/neutrophilic character of radicals has been shown in a variety of instances. One example is the alternating tendency of the copolymerization of maleic
anhydride (electrophilic) and styrene (slightly nucleophilic).
In intramolecular reactions, precise control can be achieved despite the extreme reactivity of radicals. In general, radicals attack the closest reactive site the most readily. Therefore,
when there is a choice, a preference for five-membered rings is observed: four-membered rings are too strained, and collisions with carbons six or more atoms away in the chain are
infrequent.
Carbenes and nitrenes, which are diradicals, have distinctive chemistry.

Combustion

Spectrum of the blue flame from a butane torch showing excited molecular radical band emission and Swan bands
A familiar free-radical reaction is combustion. The oxygen molecule is a stable diradical, best represented by ·O-O·. Because spins of the electrons are parallel, this molecule is stable.
While the ground stateof oxygen is this unreactive spin-unpaired (triplet) diradical, an extremely reactive spin-paired (singlet) state is available. For combustion to occur, the energy
barrier between these must be overcome. This barrier can be overcome by heat, requiring high temperatures. The triplet-singlet transition is also "forbidden". This presents an additional
barrier to the reaction. It also means molecular oxygen is relatively unreactive at room temperature except in the presence of a catalytic heavy atom such as iron or copper.
Combustion consists of various radical chain reactions that the singlet radical can initiate. The flammability of a given material strongly depends on the concentration of free radicals
that must be obtained before initiation and propagation reactions dominate leading to combustion of the material. Once the combustible material has been consumed, termination
reactions again dominate and the flame dies out. As indicated, promotion of propagation or termination reactions alters flammability. For example, because lead itself deactivates free
radicals in the gasoline-air mixture, tetraethyl lead was once commonly added to gasoline. This prevents the combustion from initiating in an uncontrolled manner or in unburnt residues
(engine knocking) or premature ignition (preignition).
When a hydrocarbon is burned, a large number of different oxygen radicals are involved. Initially, hydroperoxyl radical (HOO·) are formed. These then react further to give organic
hydroperoxides that break up into hydroxyl radicals (HO·).

Polymerization
In addition to combustion, many polymerization reactions involve free radicals. As a result many plastics, enamels, and other polymers are formed through radical polymerization. For
instance, drying oils and alkyd paints harden due to radical crosslinking by oxygen from the atmosphere.
Recent advances in radical polymerization methods, known as living radical polymerization, include:
Reversible addition-fragmentation chain transfer (RAFT)
Atom transfer radical polymerization (ATRP)
Nitroxide mediated polymerization (NMP)
These methods produce polymers with a much narrower distribution of molecular weights.

Atmospheric radicals
The most common radical in the lower atmosphere is molecular dioxygen. Photodissociation of source molecules produces other free radicals. In the lower atmosphere, the most
important examples of free radical production are the photodissociation of nitrogen dioxide to give an oxygen atom and nitric oxide (see eq. 1 below), which plays a key role in smog
formation—and the photodissociation of ozone to give the excited oxygen atom O(1D) (see eq. 2 below). The net and return reactions are also shown (eq. 3 and 4, respectively).

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In the upper atmosphere, a particularly important source of radicals is the photodissociation of normally unreactive chlorofluorocarbons (CFCs) by solar ultraviolet radiation, or by
reactions with other stratospheric constituents (see eq. 1 below). These reactions give off the chlorine radical, Cl•, which reacts with ozone in a catalytic chain reaction ending in Ozone
depletion and regeneration of the chlorine radical, allowing it to reparticipate in the reaction (see eq. 2–4 below). Such reactions are believed to be the primary cause of depletion of the
ozone layer (the net result is shown in eq. 5 below), and this is why the use of chlorofluorocarbons as refrigerants has been restricted.

In biology
Free radicals play an important role in a number of biological processes. Many of these are necessary for life, such as the intracellular killing of bacteria by phagocytic cells such as
granulocytes and macrophages. Researchers have also implicated free radicals in certain cell signalling processes,[6] known as redox signaling.
The two most important oxygen-centered free radicals are superoxide and hydroxyl radical. They derive from molecular oxygen under reducing conditions. However, because of their
reactivity, these same free radicals can participate in unwanted side reactions resulting in cell damage. Excessive amounts of these free radicals can lead to cell injury and death, which
may contribute to many diseases such as cancer, stroke, myocardial infarction, diabetes and major disorders.[7] Many forms of cancer are thought to be the result of reactions between
free radicals and DNA, potentially resulting in mutations that can adversely affect the cell cycle and potentially lead to malignancy.[8] Some of the symptoms of aging such as
atherosclerosis are also attributed to free-radical induced oxidation of cholesterol to 7-ketocholesterol.[9] In addition free radicals contribute to alcohol-induced liver damage, perhaps
more than alcohol itself. Free radicals produced by cigarette smoke are implicated in inactivation of alpha 1-antitrypsin in the lung. This process promotes the development of
emphysema.
Free radicals may also be involved in Parkinson's disease, senile and drug-induced deafness, schizophrenia, and Alzheimer's.[10] The classic free-radical syndrome, the iron-storage
disease hemochromatosis, is typically associated with a constellation of free-radical-related symptoms including movement disorder, psychosis, skin pigmentary melanin abnormalities,
deafness, arthritis, and diabetes mellitus. The free-radical theory of aging proposes that free radicals underlie the aging process itself. Similarly, the process of mitohormesis suggests
that repeated exposure to free radicals may extend life span.
Because free radicals are necessary for life, the body has a number of mechanisms to minimize free-radical-induced damage and to repair damage that occurs, such as the enzymes
superoxide dismutase, catalase, glutathione peroxidase and glutathione reductase. In addition, antioxidants play a key role in these defense mechanisms. These are often the three
vitamins, vitamin A, vitamin C and vitamin E and polyphenol antioxidants. Furthermore, there is good evidence indicating that bilirubin and uric acid can act as antioxidants to help
neutralize certain free radicals. Bilirubin comes from the breakdown of red blood cells' contents, while uric acid is a breakdown product of purines. Too much bilirubin, though, can lead
to jaundice, which could eventually damage the central nervous system, while too much uric acid causes gout.[11]

Reactive oxygen species

Reactive oxygen species or ROS are species such as superoxide, hydrogen peroxide, and hydroxyl radical and are associated with cell damage. ROS form as a natural by-product of the
normal metabolism of oxygen and have important roles in cell signaling.
Oxybenzone has been found to form free radicals in sunlight, and therefore may be associated with cell damage as well. This only occurred when it was combined with other ingredients
commonly found in sunscreens, like titanium oxide and octyl methoxycinnamate.[12]

Loose definition of radicals

In most fields of chemistry, the historical definition of radicals contends that the molecules have nonzero spin. However in fields including spectroscopy, chemical reaction, and
astrochemistry, the definition is slightly different. Gerhard Herzberg, who won the Nobel prize for his research into the electron structure and geometry of radicals, suggested a looser
definition of free radicals: "any transient (chemically unstable) species (atom, molecule, or ion)".[13] The main point of his suggestion is that there are many chemically unstable
molecules that have zero spin, such as C2, C3, CH2 and so on. This definition is more convenient for discussions of transient chemical processes and astrochemistry; therefore
researchers in these fields prefer to use this loose definition.[14]

Diagnostics
Free radical diagnostic techniques include:
Electron spin resonance

A widely used technique for studying free radicals, and other paramagnetic species, is electron spin resonance spectroscopy (ESR). This is alternately referred to as "electron
paramagnetic resonance" (EPR) spectroscopy. It is conceptually related to nuclear magnetic resonance, though electrons resonate with higher-frequency fields at a given fixed
magnetic field than do most nuclei.

Nuclear magnetic resonance using a phenomenon called CIDNP

Chemical labelling

Chemical labelling by quenching with free radicals, e.g. with nitric oxide (NO) or DPPH (2,2-diphenyl-1-picrylhydrazyl), followed by spectroscopic methods like X-ray
photoelectron spectroscopy (XPS) or absorption spectroscopy, respectively.

Use of free radical markers

Stable, specific or non-specific derivates of physiological substances can be measured e.g. lipid peroxidation products (isoprostanes, TBARS), amino acid oxidation products (meta-
tyrosine, ortho-tyrosine, hydroxy-Leu, dityrosine etc.), peptide oxidation products (oxidized glutathione – GSSG)
2,2'-Azobis(2-amidinopropane) dihydrochloride (AAPH) is a chemical compound used to study the chemistry of the oxidation of drugs.[15] It is a free radical-generating azo
compound. It is gaining prominence as a model oxidant in small molecule and proteintherapeutics for its ability to initiate oxidation reactions via both nucleophilic and free radical
mechanisms.[16]

Indirect method

Measurement of the decrease in the amount of antioxidants (e.g. TAS, reduced glutathione – GSH)

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 Trapping agents

Using a chemical species that reacts with free radicals to form a stable product that can then be readily measured (Hydroxyl radical and salicylic acid)

See also
-yl
Electron pair
Globally Harmonized System of Classification and Labelling of Chemicals
Hofmann–Löffler reaction

References
1. Jump up^ Oakley, Richard T. (1988). "Cyclic and Heterocyclic Thiazenes" (PDF). Progress in Inorganic Chemistry. Progress in Inorganic Chemistry 36. pp. 299–
391.doi:10.1002/9780470166376.ch4. ISBN 978-0-470-16637-6.
2. Jump up^ Rawson, J; Banister, A; Lavender, I (1995). "The Chemistry of Dithiadiazolylium and Dithiadiazolyl Rings". Advances in Heterocyclic Chemistry Volume 62. Advances
in Heterocyclic Chemistry 62. pp. 137–247. doi:10.1016/S0065-2725(08)60422-5. ISBN 978-0-12-020762-6.
3. Jump up^ Griller, David; Ingold, Keith U. (1976). "Persistent carbon-centered radicals". Accounts of Chemical Research 9: 13.doi:10.1021/ar50097a003.
4. Jump up^ Lomnicki S.; Truong H.; Vejerano E.; Dellinger B. (2008). "Copper oxide-based model of persistent free radical formation on combustion-derived particulate matter".
Environ. Sci. Technol. 42 (13): 4982–4988. doi:10.1021/es071708h.PMID 18678037.
5. Jump up^ However, paramagnetism does not necessarily imply radical character.
6. Jump up^ Pacher P, Beckman JS, Liaudet L (2007). "Nitric oxide and peroxynitrite in health and disease". Physiol. Rev. 87 (1): 315–424. doi:10.1152/physrev.00029.2006. PMC
2248324.PMID 17237348.
7. Jump up^ Rajamani Karthikeyan, Manivasagam T, Anantharaman P, Balasubramanian T, Somasundaram ST (2011). "Chemopreventive effect of Padina boergesenii extracts on
ferric nitrilotriacetate (Fe-NTA)-induced oxidative damage in Wistar rats". J. Appl. Phycol. 23, Issue 2, Page 257 (2): 257–263.doi:10.1007/s10811-010-9564-0.
8. Jump up^ Mukherjee, P. K., Marcheselli, V. L., Serhan, C. N., & Bazan, N. G. (2004). Neuroprotecin D1: A docosahexanoic acid-derived docosatriene protects human retinal
pigment epithelial cells from oxidative stress. Proceedings of the National Academy of Sciences of the USA, 101(22), 8491–8496.doi:10.1073/pnas.0402531101
9. Jump up^ http://www.ncbi.nlm.nih.gov/pubmed/10224662
10. Jump up^ Floyd, R. A., (1999). Neuroinflammatory processes are important in neurodegenerative diseases: An hypothesis to explain the increased formation of reactive oxygen and
nitrogen species as major factors involved in neurodegenerative disease development. Free Radical Biology and Medicine, 26(9–10), 1346–1355. doi:10.1016/S0891-
5849(98)002937
11. Jump up^ An overview of the role of free radicals in biology and of the use of electron spin resonance in their detection may be found in Rhodes C.J. (2000). Toxicology of the
Human Environment – the critical role of free radicals. London: Taylor and Francis.ISBN 0-7484-0916-5.
12. Jump up^ Serpone N, Salinaro A, Emeline AV, Horikoshi S, Hidaka H, Zhao JC. 2002. An in vitro systematic spectroscopic examination of the photostabilities of a random set of
commercial sunscreen lotions and their chemical UVB/UVA active agents. Photochemical & Photobiological Sciences 1(12): 970-981.
13. Jump up^ G. Herzberg (1971), "The spectra and structures of simple free radicals", ISBN 0-486-65821-X.
14. Jump up^ 28th International Symposium on Free Radicals.
15. Jump up^ Betigeri, Seema; Thakur, Ajit; Raghavan, Krishnaswamy (2005). "Use of 2,2?-Azobis(2-Amidinopropane) Dihydrochloride as a Reagent Tool for Evaluation of
Oxidative Stability of Drugs".Pharmaceutical Research 22 (2): 310–7. doi:10.1007/s11095-004-1199-x. PMID 15783080.
16. Jump up^ Werber, Jay; Wang, Y. John; Milligan, Michael; Li, Xiaohua; Ji, Junyan A. (2011). "Analysis of 2,2′-azobis (2-amidinopropane) dihydrochloride degradation and
hydrolysis in aqueous solutions". Journal of Pharmaceutical Sciences 100(8): 3307–15. doi:10.1002/jps.22578. PMID 21560126.

Further Reading

MasterOrganicChemistry
3 Factors That Stabilize Free Radicals
What Factors Destabilize Free Radicals?
In Summary: Free Radicals
Carey 4th Edition On-Line Activity
More about Radicals
Slide Presentations
Free Radical Lecture
Web Pages
Homolytic Cleavage Definition
Homolytic and Heterolytic Cleavage
6.3 Free Radicals is shared under a CC BY-NC-SA 4.0 license and was authored, remixed, and/or curated by LibreTexts.
Free Radicals is licensed CC BY-NC-SA 4.0.

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 CHAPTER OVERVIEW

Chapter 7. Reactivity and Electron Movement

Purdue CHM 26505: Organic

Chemistry for Chemistry Majors (1st
Semester)
Fall 2014: Prof. Mark Lipton

Template:HideTOC

Topic hierarchy
7.1 Nucleophiles and Electrophiles
7.2 How Electrons Move
7.3 Basics of Thermodynamics and Kinetics
7.4 Kinetics
7.5 Product Distributions
7.6 Hammond's Postulate

Chapter 7. Reactivity and Electron Movement is shared under a CC BY-NC-SA 4.0 license and was authored, remixed, and/or curated by LibreTexts.

1
7.1 Nucleophiles and Electrophiles
Nucleophiles
What is a 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.
Now, lets discuss some of the major factors that affect nucleophilicity.

Protonation states and nucleophilicity

The protonation state of a nucleophilic atom has a very large effect on its nucleophilicity. This is an idea that makes intuitive sense:
a hydroxide ion is much more nucleophilic (and basic) than a water molecule, because the negatively charged oxygen on the
hydroxide ion carries greater electron density than the oxygen atom of a neutral water molecule. In practical terms, this means that
a hydroxide nucleophile will react in an SN2 reaction with methyl bromide much faster ( about 10,000 times faster) than a water
nucleophile.

Periodic trends and solvent effects in nucleophilicity

There are predictable periodic trends in nucleophilicity. Moving horizontally across the second row of the table, the trend in
nucleophilicity parallels the trend in basicity:

The reasoning behind the horizontal nucleophilicity trend is the same as the reasoning behind the basicity trend: more
electronegative elements hold their electrons more tightly, and are less able to donate them to form a new bond.
This horizontal trends also tells us that amines are more nucleophilic than alcohols, although both groups commonly act as
nucleophiles in both laboratory and biochemical reactions.
Recall that the basicity of atoms decreases as we move vertically down a column on the periodic table: thiolate ions are less basic
than alkoxide ions, for example, and bromide ion is less basic than chloride ion, which in turn is less basic than fluoride ion. Recall
also that this trend can be explained by considering the increasing size of the 'electron cloud' around the larger ions: the electron
density inherent in the negative charge is spread around a larger area, which tends to increase stability (and thus reduce basicity).
The vertical periodic trend for nucleophilicity is somewhat more complicated that that for basicity: depending on the solvent that
the reaction is taking place in, the nucleophilicity trend can go in either direction. Let's take the simple example of the SN2 reaction
below:

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. . .where Nu- is one of the halide ions: fluoride, chloride, bromide, or iodide, and the leaving group I* is a radioactive isotope of
iodine (which allows us to distinguish the leaving group from the nucleophile in that case where both are iodide). If this reaction is
occurring in a protic solvent (that is, a solvent that has a hydrogen bonded to an oxygen or nitrogen - water, methanol and ethanol
are the most important examples), then the reaction will go fastest when iodide is the nucleophile, and slowest when fluoride is the
nucleophile, reflecting the relative strength of the nucleophile.

Relative nucleophilicity in a protic solvent

This of course, is opposite that of the vertical periodic trend for basicity, where iodide is the least basic. What is going on here?
Shouldn't the stronger base, with its more reactive unbonded valence electrons, also be the stronger nucleophile?
As mentioned above, it all has to do with the solvent. Remember, we are talking now about the reaction running in a protic solvent
like ethanol. Protic solvent molecules form very strong ion-dipole interactions with the negatively-charged nucleophile, essentially
creating a 'solvent cage' around the nucleophile:

In order for the nucleophile to attack the electrophile, it must break free, at least in part, from its solvent cage. The lone pair
electrons on the larger, less basic iodide ion interact less tightly with the protons on the protic solvent molecules - thus the iodide
nucleophile is better able to break free from its solvent cage compared the smaller, more basic fluoride ion, whose lone pair
electrons are bound more tightly to the protons of the cage.
The picture changes if we switch to a polar aprotic solvent, such as acetone, in which there is a molecular dipole but no hydrogens
bound to oxygen or nitrogen. Now, fluoride is the best nucleophile, and iodide the weakest.

Relative nucleophilicity in a polar aprotic solvent

The reason for the reversal is that, with an aprotic solvent, the ion-dipole interactions between solvent and nucleophile are much
weaker: the positive end of the solvent's dipole is hidden in the interior of the molecule, and thus it is shielded from the negative
charge of the nucleophile.

A weaker solvent-nucleophile interaction means a weaker solvent cage for the nucleophile to break through, so the solvent effect is
much less important, and the more basic fluoride ion is also the better nucleophile.
Why not use a completely nonpolar solvent, such as hexane, for this reaction, so that the solvent cage is eliminated completely?
The answer to this is simple - the nucleophile needs to be in solution in order to react at an appreciable rate with the electrophile,
and a solvent such as hexane will not solvate an a charged (or highly polar) nucleophile at all. That is why chemists use polar
aprotic solvents for nucleophilic substitution reactions in the laboratory: they are polar enough to solvate the nucleophile, but not so

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polar as to lock it away in an impenetrable solvent cage. In addition to acetone, three other commonly used polar aprotic solvents
are acetonitrile, dimethylformamide (DMF), and dimethyl sulfoxide (DMSO).

In biological chemistry, where the solvent is protic (water), the most important implication of the periodic trends in nucleophilicity
is that thiols are more powerful nucleophiles than alcohols. The thiol group in a cysteine amino acid, for example, is a powerful
nucleophile and often acts as a nucleophile in enzymatic reactions, and of course negatively-charged thiolates (RS-) are even more
nucleophilic. This is not to say that the hydroxyl groups on serine, threonine, and tyrosine do not also act as nucleophiles - they do.

Resonance effects on nucleophilicity

Resonance effects also come into play when comparing the inherent nucleophilicity of different molecules. The reasoning involved
is the same as that which we used to understand resonance effects on basicity. If the electron lone pair on a heteroatom is
delocalized by resonance, it is inherently less reactive - meaning less nucleophilic, and also less basic. An alkoxide ion, for
example, is more nucleophilic and more basic than a carboxylate group, even though in both cases the nucleophilic atom is a
negatively charged oxygen. In the alkoxide, the negative charge is localized on a single oxygen, while in the carboxylate the charge
is delocalized over two oxygen atoms by resonance.

The nitrogen atom on an amide is less nucleophilic than the nitrogen of an amine, due to the resonance stabilization of the nitrogen
lone pair provided by the amide carbonyl group.

Steric effects on nucleophilicity

Steric hindrance is an important consideration when evaluating nucleophility. For example, tert-butanol is less potent as a
nucleophile than methanol. This is because the comparatively bulky methyl groups on the tertiary alcohol effectively block the
route of attack by the nucleophilic oxygen, slowing the reaction down considerably (imagine trying to walk through a narrow
doorway while carrying three large suitcases!).

It is not surprising that it is more common to observe serines acting as nucleophiles in enzymatic reactions compared to threonines
- the former is a primary alcohol, while the latter is a secondary alcohol.

Example

Which is the better nucleophile - a cysteine side chain or a methionine side chain? Explain.

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 Example

In each of the following pairs of molecules/ions, which is the better nucleophile in a reaction with CH3Br in acetone solvent? Explain your choice.
a. phenolate ion (deprotonated phenol) or benzoate ion (deprotonated benzoic acid)
b. water and hydronium ion
c. trimethylamine and triethylamine
d. chloride anion and iodide anion
e. CH3NH- and CH3CH2NH

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.

Consider two hypothetical SN2 reactions: one in which the electrophile is a methyl carbon and another in which it is tertiary carbon.

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.

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.

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Further Reading

MasterOrganicChemistry
Nucleophiles and Electrophiles
What Makes a Good Nucleophile?
The Three Classes of Nucleophile

Carey 4th Edition Online

Nucleophiles

Khan Academy
Nucleophiles and Electrophiles and the Schwartz Rule

Websites
Wikipedia - Nucleophile
Electrophiles and Nucleophiles Tutorial

Videos
Nucleophiles and Electrophiles
7.1 Nucleophiles and Electrophiles is shared under a CC BY-NC-SA 4.0 license and was authored, remixed, and/or curated by LibreTexts.
Nucleophiles is licensed CC BY-NC-SA 4.0.
Electrophiles is licensed CC BY-NC-SA 4.0.

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7.2 How Electrons Move
The Correct Use of Arrows to Indicate Electron Movement
The ability to write an organic reaction mechanism properly is key to success in organic chemistry classes. Organic chemists use a
technique called arrow pushing to depict the flow or movement of electrons during chemical reactions. Arrow pushing helps
chemists keep track of the way in which electrons and their associated atoms redistribute as bonds are made and broken. The first
essential rule to keep in mind is the following:
First rule: Arrows are used to indicate movement of electrons
A regular arrow (double-sided arrowhead) is used to indicate the movement of two electrons, while a line with a single-sided
arrowhead (sometimes called a “fish hook arrow”) is used for single electron movement involved with radical reactions that
are first described in Chapter 8.

The great majority of reactions that will be discussed in this book involve movement of pairs of electrons, so they are
represented by double-sided arrowheads.
Arrow pushing was first introduced in Section 1.8A in the discussion of resonance contributing structures. Recall that when
comparing two or more contributing structures, an arrow was used to show how two electrons (lines representing bonds or
pairs of dots representing lone pairs) could be redistributed within a single chemical structure to create an alternative Lewis
line structure representation of the bonding. By convention, arrows are used to keep track of all pairs of electrons that are in
different locations in the two different contributing Lewis line structures, shown here for the acetate anion and benzene
molecule.

Keep in mind that in the case of resonance, 1) the atoms do not move between contributing structures, and 2) the electrons
are not actually moving. The true chemical structure should be thought of as a hybrid of the contributing Lewis line
structures. It is worth pointing out that when used with contributing structures, arrows generally indicate only the
interconversion of p bonds and lone pairs (acetate ions) or just p bonds (benzene), not the formation or breaking of s bonds.
In chemical reactions, both electrons and atoms change positions as both p and s bonds are formed and broken. Arrow
pushing is used to keep track of the movement of all electrons involved with each step of the overall transformation. Because
electrons are located in orbitals surrounding atoms, when bonds are formed or broken, the movement of electrons between
orbitals is necessarily accompanied by the movement of the associated atoms, which leads to the second rule of arrow
pushing when depicting chemical reaction mechanisms:
Second Rule: Arrows are never used to indicate the movement of atoms directly. The arrows only show atom movement indirectly
as a consequence of electron movement when covalent bonds are made and broken.
We have already used arrow pushing to show proton transfer several times in Chapter 4. The example below shows the
transfer of a proton from the relatively acidic acetic acid molecule to the relatively basic hydroxide anion. We show this
process with one arrow (labeled “a” in the diagram) that starts at a lone pair of electrons on the basic oxygen atom of the
hydroxide anion, then points to the acidic H atom of acetic acid to indicate formation of the new bond being made. A second
arrow originates at the line representing the breaking O-H bond and points to the O atom to denote creation of a lone pair

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 (arrow “b”). In this reaction, the proton is being transferred between molecules, and the arrows indicate movement of the
electrons involved.

A common mistake beginning students make is that they will erroneously write an arrow pointing from the H of the acetic
acid to the O atom of the hydroxide anion. This is wrong, because such an arrow would be indicating the H atom movement
directly, not electron movement! Other common mistakes in arrow pushing are given at the end.

Electron Sources and Sinks: How to Predict What Will Occur in an Organic Reaction Mechanism
Combined with the arrows shown for the contributing structures shown previously, we have now seen all three of the situations
illustrated by arrows with double-sided arrowheads, namely the redistribution of p bonds and/or lone pairs, formation of a new s
bond (generally from a lone pair or sometimes a new p bond), and breaking of a s bond (generally to form a new lone pair or
sometimes a new p bond). Often, as in the case of the acetate-hydroxide ion reaction, more than one arrow is used in a given
mechanism step. Now that you have seen all of the important types of arrows, we can point out the most important common feature
between them:
Third Rule: Arrows always start at an electron source and end at an electron sink.

An electronsource is a bond or a lone pair of electrons. It is either a p bond or a lone pair on an atom of relatively high
electron density in a molecule or ion, or a bond that must break during a reaction. An electron sink is an atom on a molecule
or ion that can accept a new bond or lone pair of electrons.
Learning to identify the characteristic sources and sinks in different functional groups is the key to learning organic
chemistry reaction mechanisms. For example, for arrows that depict the formation of new s bonds, the electron source is
often readily identified as being a lone pair on the most electron rich atom of a molecule or ion, and the electron sink is
readily identified as the most electron poor atom of a molecule or ion. Thus, the prediction of many of the most important
electron sources and sinks comes down to lessons concerning the differences in electronegativity between atoms that were
presented in Section 1.2, which allow you to identify partial and formal negative and positive charges in molecules. As an aid
to your analysis, the red and blue colors of the various electrostatic surface maps given throughout this book indicate the
negative and positive regions of molecules. We will have more to say about this reactivity pattern a little bit later.
This leads us to another commonly encountered type of process that deserves mention. As you will see in this and many later
chapters, making a new bond to an electron sink often requires the simultaneous breaking of one of the bonds present at the
sink atom to avoid overfilling its valence orbitals, a situation referred to as hypervalence.
Fourth rule: Breaking a bond will occur to avoid overfilling valence (hypervalence) on an atom serving as an electron sink.
In these cases, the electron source for the arrow is the bond being broken, and the sink is an atom able to accommodate the
electrons as a lone pair, generally an electronegative atom such as an O atom or a halogen. If an ion is created, that ion is
often stabilized by resonance delocalization or other stabilizing interactions.
Returning to the proton transfer reaction between acetic acid and hydroxide, we can now summarize our analysis of this
simple one-step mechanism.

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Viewed in the context of the third rule, when considering the arrow used to make a new s bond (arrow a), the hydroxide O atom is
the electron source (most negatively charged atom) and the acetic acid H atom is the electron sink (atom with highest partial
positive charge). This is illustrated using the electrostatic molecular surfaces shown below the reaction equation. The O atom of
hydroxide ion has the greatest localized negative charge as indicated by the most intense red color and the acetic acid proton being
transferred has the most intense positive charge character indicated by the most intense blue color. In order to avoid overfilling the
valence of the H atom during the reaction (fourth rule), the O-H bond of acetic acid must be broken (arrow “b”). In so doing, the
acetate ion is formed. Note that the acetate ion is stabilized by resonance delocalization.
Based on our analysis of the reaction between acetic acid and the hydroxide anion, you should now appreciate that the transfer of a
proton (a so-called Brønsted acid-base reaction) is really just a special case of the common pattern of reactivity between an electron
source (the base) and the proton as an electron sink, combined with breaking a bond to satisfy valence and create a relatively stable
ion.
The addition or removal of protons during chemical reactions is so common that proton transfer steps are referred to by name
directly, and we will use phrases such as “add a proton” or “take a proton away” when referring to them. However, proton transfer
reactions are not the only case in which we use special names to describe a particular type of common reaction that involves arrows
between electron sources and electron sinks.
As briefly mentioned in Section 4.7, a broader terminology is applied to the very common case of reactions in which new s bonds
form between electron rich and electron poor regions of molecules. Nucleophiles (meaning nucleus seeking) are molecules that
have relatively electron rich p bonds or lone pairs that act as electron sources for arrows making new bonds. Electrophiles
(meaning electron seeking) are molecules with relatively electron poor atoms that serve as sinks for these arrows. Analogously, a
molecule, or region of a molecule, that is a source for such an arrow is called nucleophilic, while a molecule or region of a
molecule that is a sink for these arrows is referred to as being electrophilic. Based on this description, it should be clear that
nucleophiles are analogous to Lewis bases and electrophiles are analogous to Lewis acids. Chemists use these terms
interchangeably, although nucleophile and electrophile are more commonly used in kinetics discussions while Lewis acid and
Lewis base are more commonly used in discussions about reaction thermodynamics. We will use all of these terms throughout the
rest of the book.
It is helpful to summarize the appropriate use of key terms associated with arrow pushing and reaction mechanisms. The terms
“source” and “sink” are used to identify the start and end of each reaction mechanism arrow, which is indicating the change in
location of electron pairs. The terms “nucleophile” and “electrophile” (as well as “Lewis base” and “Lewis acid”) are used to
describe molecules based on their chemical reactivity and propensity to either donate or receive electrons when they interact.
Protons can be thought of as a specific type of electrophile, and for reactions in which a proton is transferred, the nucleophile is
called a base.

Example 1: I see you

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 The following two sets of reactions (A and B) show possibilities for arrow pushing in individual reaction steps. Identify which is wrong and
explain why. Next, using arrow pushing correctly, label which molecule is the nucleophile and which is the electrophile.

Solution
In each case the first arrow pushing scenario is wrong. The arrows shown below with stars over them do not start at a source of electrons, but
rather they start at positions of relative positive charge, which is incorrect.

In the correct arrow pushing, the arrow labeled “a” depicts the interaction of a region of relative high negative charge (a p-bond or lone pair) with
an atom of relatively high partial positive charge on the other reactant. Therefore, the molecule acting as the source for arrow the s bond-forming
arrow “a” is the nucleophile while the molecule containing the sink atom is the electrophile. The arrow labeled “b” is needed to satisfy valence,
and is not considered when defining the nucleophile and electrophile.

Putting it All Together: It Comes Down to a Multiple Choice Situation

In the sections and chapters that follow, many different reaction mechanisms will be described in a stepwise fashion. Each arrow
can be classified according to one of the three overall situations we have already encountered (redistribution of π bonds and/or lone
pairs, formation of a new s bond from a lone pair or π bond, breaking a s bond to give a new lone pair or π bond).
When learning new mechanisms, first focus on the overall transformation that takes place. It might be a reaction in which atoms or
groups are added (an addition reaction), a reaction in which atoms or groups are removed (an elimination reaction), a reaction in
which atoms or groups replace an atom or group (a substitution reaction), or other processes we will encounter. Often, the overall
process is composed of multiple steps. Once you have the overall process in mind, it is time to think about the individual steps that
convert starting material(s) into product(s). Predicting complete multi-step mechanisms, then, comes down to learning how to
predict the individual steps.
Understanding, as opposed to memorizing, mechanisms is critical to mastering organic chemistry. Although the mechanisms you
encounter throughout the course may seem entirely different, they are actually related in fundamental ways. In fact, almost all of
the organic reaction mechanisms you will learn are composed of only a few different individual elements (steps) that are put
together in various combinations. Your job is to learn these individual mechanism elements, and then understand how to assemble
them into the steps of the correct mechanism for the overall reaction.
Fortunately, there are a surprisingly small number of different types of characteristic mechanism elements (patterns of arrows) to be
considered when trying to predict individual steps of even complex chemical reactions. For this reason, you should view the
prediction of each step in an organic mechanism as essentially a multiple choice situation in which your most common choices are
the following:
1. Make a new bond between a nucleophile (source for an arrow) and an electrophile (sink for an arrow). Use this element
when there is a nucleophile present in the solution as well as an electrophile suitable for reaction to occur.

1. Break a bond so that relatively stable molecules or ions are created Use this element when there is no suitable nucleophile-
electrophile or proton transfer reaction, but breaking a bond can create neutral molecules or relatively stable ions, or both.

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 1. Add a proton Use this element when there is no suitable nucleophile-electrophile reaction, but the molecule has a strongly
basic functional group or there is a strong acid present.

1. Take a proton away Use this element when there is no suitable nucleophile-electrophile reaction, but the molecule has a
strongly acidic proton or there is a strong base present.

The situation is even simpler than you might expect because 1. and 2. are the functional reverse of each other, as are 3. and 4. in
many cases.
Many times, more than one of the four choices occurs simultaneously in the same mechanism step and there are some special
situations in which unique or different processes such as electrophilic addition or 1,2 shifts occur. These different processes are
described in detail as they are encountered.
In the following sections and chapters of the book, you will learn important properties of the different functional groups that allow
you to deduce the appropriate choices for the individual steps in reaction mechanisms. To help you accomplish this, as new
mechanisms are introduced throughout the rest of the book, we will label each mechanistic step as one of the four mentioned here
when appropriate, emphasizing the common features between even complex mechanisms. When you are able to predict which of
the above choices is(are) the most appropriate for a given step in a mechanism, you will then be able to push electrons correctly
without relying on memorization. At that point, you will have taken a major step toward mastering organic chemistry!

Common Mistakes in Arrow Pushing

Throughout this book arrow pushing is used to indicate the flow of electrons in the various organic reaction mechanisms that are
discussed. A few simple rules for properly performing arrow pushing were introduced in Section 6.2. In this Appendix we examine
some of the most common mistakes that students make when first learning arrow-pushing methods and tell you how to avoid them.
The mistakes given below are the ones seen most often by the authors during their cumulative dozens of year of experience in
teaching Introductory Organic Chemistry.

Backwards Arrows
Reversing the direction of one or more arrows during a chemical step is the most common mistake made by students when writing
organic reaction mechanisms. Backwards arrow pushing usually derives from a student thinking about the movement of atoms, not
the movement of electrons. Hence, to avoid this mistake it is important to remember that arrows depict how electrons move, not
where atoms move, within or between chemical structures. Further, one can avoid this mistake by remembering that every arrow
must start at an electron source (a bond or lone pair) and terminate at an electron sink (an atom that can accept a new bond or lone
pair).

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Not Enough Arrows
A second common mistake in writing arrow-pushing schemes is to not use enough arrows. This usually results from not keeping
track of all lone pairs, bonds made, or bonds broken in a mechanism step. In other words, if you analyze exactly the new position of
electrons resulting from each arrow, missing arrows will become evident. In the following example we compare two arrow-pushing
scenarios, one of which is missing an arrow. In the incorrect scheme there is no arrow that indicates breaking of the C-H bond of
the reactant and formation of the p-bond in the alkene product. Note that when an arrow is missing, the result is commonly too
many bonds and/or lone pairs on one atom (see the next section on hypervalency) and not enough bonds or lone pairs on another.

Hypervalency
Another frequent mistake when writing arrow-pushing schemes is to expand the valency of an atom to more electrons than an atom
can accommodate, a situation referred to as hypervalency. An overarching principle of organic chemistry is that carbon has eight
electrons in its valence shell when present in stable organic molecules (the Octet Rule, Section 1.2). Analogously, many of the
other most common elements in organic molecules, such as nitrogen, oxygen, and chlorine, also obey the Octet Rule. There are
three common ways in which students incorrectly draw hypervalent atoms: 1) Too many bonds to an atom, 2) Forgetting the
presence of hydrogens, and 3) Forgetting the presence of lone pairs.
In the following case an arrow is used to depict a potential resonance structure of nitromethane. However, the result is a nitrogen
atoms with 10 electrons in its valence shell because there are too many bonds to N. Such mistakes can be avoided by remembering
to draw all bonds and lone pairs on an atom so that the total number of electrons in each atoms valence shell is apparent.

Another common way students mistakenly end up with a hypervalent atom is to forget the presence of hydrogens that are not
explicitly written. When using stick diagrams to write organic chemical structures not all the hydrogens are drawn, and hence it is
common to forget them during an arrow pushing exercise. The following example shows two proposed resonance contributing
structures of an amide anion. The arrow drawn on the molecule to the left is incorrect because it depicts the formation of a new
bond to a carbon that already has four bonds. When both bonds to hydrogen are drawn explicitly as on the structure farthest to the
right, it is clear there are now five bonds around the indicated carbon atom. Notice also that the negative charge was lost upon
drawing the contributing structures on the right, providing another clear signal that something was wrong because overall charge is
always conserved when arrows are drawn correctly.

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Another common way to make a hypervalency mistake is by forgetting to count all lone pairs of electrons. The following example
shows a negatively charged nucleophile incorrectly adding to the formal positive charge on an alkylated ketone. This may look
correct because atoms with positive and negative charges are being directly combined, but when counting bonds and lone pairs of
electrons, it is found that the oxygen ends up with 10 electrons overall. Hence, this is a mistake.

Mixed Media Errors

Acids and bases are catalysts, reactants, products, and intermediates in many organic chemistry transformations. When writing
mechanisms for reactions involving acids and bases, there are three general rules that will help guide you in depicting the correct
mechanism.
Do not show the creation of a strong acid for a mechanism of a reaction that is performed in strongly basic media.
Do not show the creation of a strong base for a mechanism of a reaction that is performed in strongly acidic media.
In strongly acidic media, all the intermediates and products will be either neutral or positively charged, while in strongly basic
media, all the products and intermediates will be neutral or negatively charged.
The reason for these rules is that significant extents of strong acids and bases cannot co-exist simultaneously in the same medium
because they would rapidly undergo a proton transfer reaction before anything else would happen in the solution.
An example of a mixed media error is given below. The first example shows a strong base being created although the reaction is
performed under acidic conditions (see conditions over the first equilibrium arrows). Not shown are the three steps that lead to the
intermediate drawn. A mistake is made in the arrow pushing because a strong base (methoxide) is generated as the leaving group
even though the reaction is run in strong acid. In the correct mechanism, the next step would be protonation of the ether oxygen
atom followed by loss of methanol in the last step (not shown) to give a carboxylic acid product.

Failing to conserve charge

Overall charge must be conserved in all mechanism steps. Failure to conserve overall charge could be caused by some of the
preceding errors (hypervalency, failure to draw arrows, mixed media errors), but we mention it by itself because it is always helpful
to check that your arrow pushing is consistent by confirming that overall charge conservation is obeyed. In the example shown
below, an arrow is missing leading to a neutral intermediate even thought the overall charge on the left side of the equation was
minus one. Notice there are five bonds to carbon on the intermediate (hypervalency), providing another obvious indication that
something was incorrect in the mechanism step as drawn.

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Contributors
Brent Iverson (UT Austin)

Further Reading

MasterOrganicChemistry
Use of Curved Arrows
How Not to Draw Resonance Curved Arrows
Curved Arrows (for Reactions)
Curved Arrows(2): Initial Tails and Final Heads

Websites
Wikipedia - Arrow Pushing
Electron Pushing in Organic Chemistry

Videos
Leah4Sci - Electron Pushing
7.2 How Electrons Move is shared under a CC BY-NC-SA 4.0 license and was authored, remixed, and/or curated by LibreTexts.
Everything You Need to Know About Mechanisms is licensed CC BY-NC-SA 4.0.

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7.3 Basics of Thermodynamics and Kinetics
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˚ (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)
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 (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.

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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 (3)

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

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This too should make some intuitive sense; if the forward rate constant is higher than the reverse rate constant, equilibrium should
lie towards products.

Further Reading

MasterOrganicChemistry
Equilibria

Websites
Reversible and irreversible reactions
7.3 Basics of Thermodynamics and Kinetics is shared under a CC BY-NC-SA 4.0 license and was authored, remixed, and/or curated by
LibreTexts.

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7.4 Kinetics
Rate Laws
Typically, reaction rates decrease with time because reactant concentrations decrease as reactants are converted to products. You
also learned that reaction rates generally increase when reactant concentrations are increased. We now examine the mathematical
expressions called rate laws, which describe the relationships between reactant rates and reactant concentrations. Rate laws are
laws that are mathematical descriptions of experimentally verifiable data.
Rate laws may be written from either of two different but related perspectives. A differential rate law expresses the reaction rate
in terms of changes in the concentration of one or more reactants (Δ[R]) over a specific time interval (Δt). In contrast, an
integrated rate law describes the reaction rate in terms of the initial concentration ([R]0) and the measured concentration of one or
more reactants ([R]) after a given amount of time (t); we will discuss integrated rate laws in Section 14.3. The integrated rate law
can be found by using calculus to integrate the differential rate law, although the method of doing so is beyond the scope of this
text. Whether you use a differential rate law or integrated rate law, always make sure that the rate law gives the proper units for the
reaction rate, usually moles per liter per second (M/s).

Reaction Orders
For a reaction with the general equation
Equation 14.8
aA + bB → cC + dD
the experimentally determined rate law usually has the following form:
Equation 14.9
rate = k[A]m[B]n
The proportionality constant (k) is called the rate constant, and its value is characteristic of the reaction and the reaction
conditions. A given reaction has a particular value of the rate constant under a given set of conditions, such as temperature,
pressure, and solvent; varying the temperature or the solvent usually changes the value of the rate constant. The numerical value of
k, however, does not change as the reaction progresses under a given set of conditions.
Thus the reaction rate depends on the rate constant for the given set of reaction conditions and the concentration of A and B raised
to the powers m and n, respectively. The values of m and n are derived from experimental measurements of the changes in reactant
concentrations over time and indicate the reaction order, the degree to which the reaction rate depends on the concentration of
each reactant; m and n need not be integers. For example, Equation 14.9 tells us that Equation 14.8 is mth order in reactant A and
nth order in reactant B. It is important to remember that n and m are not related to the stoichiometric coefficients a and b in the
balanced chemical equation and must be determined experimentally. The overall reaction order is the sum of all the exponents in
the rate law: m + n.

Note the Pattern

Under a given set of conditions, the value of the rate constant does not change as the reaction progresses.
Although differential rate laws are generally used to describe what is occurring on a molecular level during a reaction, integrated
rate laws are used to determine the reaction order and the value of the rate constant from experimental measurements. (We present
general forms for integrated rate laws) To illustrate how chemists interpret a differential rate law, we turn to the experimentally
derived rate law for the hydrolysis of t-butyl bromide in 70% aqueous acetone. This reaction producest-butanol according to the
following equation:
(C H3 )3 C Br(soln) + H2 O(soln) → (C H3 )3 C OH(soln) + H Br(soln) (14.10)

Combining the rate expression in Equation 14.4 and Equation 14.9 gives us a general expression for the differential rate law:
Δ[A]
m n
rate = − = k[A] [B] (14.11)
Δt

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Inserting the identities of the reactants into Equation 14.11 gives the following expression for the differential rate law for the
reaction:
Δ[(C H3 )3 CBr]
m n
rate = − = k[(C H3 )3 CBr] [ H2 O] (14.12)
Δt

Experiments done to determine the rate law for the hydrolysis of t-butyl bromide show that the reaction rate is directly proportional
to the concentration of (C H ) C Br but is independent of the concentration of water. Thus m and n in Equation 14.12 are 1 and 0,
3 3

respectively, and
1 0
rate = k[(C H3 )3 C Br] [ H2 O] = k[(C H3 )3 C Br] (14.13)

Because the exponent for the reactant is 1, the reaction is first order in (CH3)3CBr. It is zeroth order in water because the exponent
for [H2O] is 0. (Recall that anything raised to the zeroth power equals 1.) Thus the overall reaction order is 1 + 0 = 1. What the
reaction orders tell us in practical terms is that doubling the concentration of (CH3)3CBr doubles the reaction rate of the hydrolysis
reaction, halving the concentration of (CH3)3CBr halves the reaction rate, and so on. Conversely, increasing or decreasing the
concentration of water has no effect on the reaction rate. (Again, when you work with rate laws, there is no simple correlation
between the stoichiometry of the reaction and the rate law. The values of k, m, and n in the rate law must be determined
experimentally.) Experimental data show that k has the value 5.15 × 10−4 s−1 at 25°C. The rate constant has units of reciprocal
seconds (s−1) because the reaction rate is defined in units of concentration per unit time (M/s). The units of a rate constant depend
on the rate law for a particular reaction.
Under conditions identical to those for the t-butyl bromide reaction, the experimentally derived differential rate law for the
hydrolysis of methyl bromide (CH3Br) is as follows:
Δ[C H3 Br]
′
rate = − = k [C H3 Br] (14.14)
Δt

This reaction also has an overall reaction order of 1, but the rate constant in Equation 14.14 is approximately 106 times smaller than
that for t-butyl bromide. Thus methyl bromide hydrolyzes about 1 million times more slowly than t-butyl bromide, and this
information tells chemists how the reactions differ on a molecular level.
Frequently, changes in reaction conditions also produce changes in a rate law. In fact, chemists often change reaction conditions to
obtain clues about what is occurring during a reaction. For example, when t-butyl bromide is hydrolyzed in an aqueous acetone
solution containing OH− ions rather than in aqueous acetone alone, the differential rate law for the hydrolysis reaction does not
change. For methyl bromide, in contrast, the differential rate law becomes rate =k″[CH3Br][OH−], with an overall reaction order of
2. Although the two reactions proceed similarly in neutral solution, they proceed very differently in the presence of a base, which
again provides clues as to how the reactions differ on a molecular level.

Note the Pattern

Differential rate laws are generally used to describe what is occurring on a molecular level during a reaction, whereas integrated
rate laws are used for determining the reaction order and the value of the rate constant from experimental measurements.

Example 3

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We present three reactions and their experimentally determined differential rate laws. For each reaction, give the units of the rate constant, give the
reaction order with respect to each reactant, give the overall reaction order, and predict what happens to the reaction rate when the concentration of
the first species in each chemical equation is doubled.
Pt

1. 2HI(g) −→ H 2 (g) + I2 (g)

1 Δ[HI]
2
rate = − ( ) = k[HI]
2 Δt

2. 2N 2 O(g) −
→ 2 N2 (g) + O2 (g)

1 Δ[N2 O]
rate = − ( ) = k
2 Δt

3. cyclopropane(g) → propane(g)
Δ[c yc lopropane ]
rate = − = k[cyclopropane]
Δt

Given: balanced chemical equations and differential rate laws

Asked for: units of rate constant, reaction orders, and effect of doubling reactant concentration
Strategy:
A Express the reaction rate as moles per liter per second [mol/(L·s), or M/s]. Then determine the units of each chemical species in the rate law.
Divide the units for the reaction rate by the units for all species in the rate law to obtain the units for the rate constant.
B Identify the exponent of each species in the rate law to determine the reaction order with respect to that species. Sum all exponents to obtain the
overall reaction order.
C Use the mathematical relationships as expressed in the rate law to determine the effect of doubling the concentration of a single species on the
reaction rate.
Solution:
1. A [HI]2 will give units of (moles per liter)2. For the reaction rate to have units of moles per liter per second, the rate constant must have
reciprocal units [1/(M·s)]:
M M/s 1
2 −1 −1
kM = k = = = M ⋅s
2
s M M⋅s

B The exponent in the rate law is 2, so the reaction is second order in HI. Because HI is the only reactant and the only species that appears in the
rate law, the reaction is also second order overall.
C If the concentration of HI is doubled, the reaction rate will increase from k[HI]02 to k(2[HI])02 = 4k[HI]02. The reaction rate will therefore
quadruple.
2. A Because no concentration term appears in the rate law, the rate constant must have M/s units for the reaction rate to have M/s units.
B The rate law tells us that the reaction rate is constant and independent of the N2O concentration. That is, the reaction is zeroth order in N2O and
zeroth order overall.
C Because the reaction rate is independent of the N2O concentration, doubling the concentration will have no effect on the reaction rate.
3. A The rate law contains only one concentration term raised to the first power. Hence the rate constant must have units of reciprocal seconds
(s−1) to have units of moles per liter per second for the reaction rate: M·s−1 = M/s.
B The only concentration in the rate law is that of cyclopropane, and its exponent is 1. This means that the reaction is first order in cyclopropane.
Cyclopropane is the only species that appears in the rate law, so the reaction is also first order overall.
C Doubling the initial cyclopropane concentration will increase the reaction rate from k[cyclopropane]0 to 2k[cyclopropane]0. This doubles the
reaction rate.
Exercise
Given the following two reactions and their experimentally determined differential rate laws: determine the units of the rate constant if time is in
seconds, determine the reaction order with respect to each reactant, give the overall reaction order, and predict what will happen to the reaction
rate when the concentration of the first species in each equation is doubled.
Δ[CH 3 N =NCH3 ]
CH 3 N =NCH3 (g) → C2 H6 (g) + N2 (g) rate = − (1)
1. Δt

= k[CH 3 N =NCH3 ] (2)

Δ[F2 ] 1 Δ[N O2 ]
2N O2 (g) + F2 (g) → 2N O2 F(g) rate = − = − ( ) (3)
2. Δt 2 Δt

= k[N O2 ][F2 ] (4)

Answer:
1. s−1; first order in CH3N=NCH3; first order overall; doubling [CH3N=NCH3] will double the reaction rate.
2. M−1·s−1; first order in NO2, first order in F2; second order overall; doubling [NO2] will double the reaction rate.

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Summary
Reaction rates are reported either as the average rate over a period of time or as the instantaneous rate at a single time.
The rate law for a reaction is a mathematical relationship between the reaction rate and the concentrations of species in solution.
Rate laws can be expressed either as a differential rate law, describing the change in reactant or product concentrations as a
function of time, or as an integrated rate law, describing the actual concentrations of reactants or products as a function of time.
The rate constant (k) of a rate law is a constant of proportionality between the reaction rate and the reactant concentration. The
power to which a concentration is raised in a rate law indicates the reaction order, the degree to which the reaction rate depends on
the concentration of a particular reactant.

Key Equations
general definition of rate for A → B
Δ[B] Δ[A]
Equation 14.4: rate = Δt
=−
Δt

general form of rate law when A and B are reactants

Equation 14.9: rate = k[A]m[B]n

Conceptual Problems

1. Explain why the reaction rate is generally fastest at early time intervals. For the second-order A + B → C, what would the plot of the
concentration of C versus time look like during the course of the reaction?
2. Explain the differences between a differential rate law and an integrated rate law. What two components do they have in common? Which form
is preferred for obtaining a reaction order and a rate constant? Why?
3. Diffusion-controlled reactions have rates that are determined only by the reaction rate at which two reactant molecules can diffuse together.
These reactions are rapid, with second-order rate constants typically on the order of 1010 L/(mol·s). Would you expect the reactions to be faster
or slower in solvents that have a low viscosity? Why? Consider the reactions H3O+ + OH− → 2H2O and H3O+ + N(CH3)3 → H2O +
HN(CH3)3+ in aqueous solution. Which would have the higher rate constant? Why?
4. What information can you get from the reaction order? What correlation does the reaction order have with the stoichiometry of the overall
equation?
5. During the hydrolysis reaction A + H2O → B + C, the concentration of A decreases much more rapidly in a polar solvent than in a nonpolar
solvent. How do you expect this effect to be reflected in the overall reaction order?

Answers

1. Reactant concentrations are highest at the beginning of a reaction. The plot of [C] versus t is a curve with a slope that becomes steadily less
positive.
3. Faster in a less viscous solvent because the rate of diffusion is higher; the H3O+/OH− reaction is faster due to the decreased relative size of
reactants and the higher electrostatic attraction between the reactants.

Numerical Problems

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 1. The reaction rate of a particular reaction in which A and B react to make C is as follows:
Δ[A] 1 Δ[C]
rate = − = ( )
Δt 2 Δt

Write a reaction equation that is consistent with this rate law. What is the rate expression with respect to time if 2A are converted to 3C?
2. While commuting to work, a person drove for 12 min at 35 mph, then stopped at an intersection for 2 min, continued the commute at 50 mph
for 28 min, drove slowly through traffic at 38 mph for 18 min, and then spent 1 min pulling into a parking space at 3 mph. What was the
average rate of the commute? What was the instantaneous rate at 13 min? at 28 min?
3. Why do most studies of chemical reactions use the initial rates of reaction to generate a rate law? How is this initial rate determined? Given the
following data, what is the reaction order? Estimate.

Time (s) [A] (M)

120 0.158

240 0.089

360 0.062

4. Predict how the reaction rate will be affected by doubling the concentration of the first species in each equation.
a. C2H5I → C2H4 + HI: rate = k[C2H5I]
b. SO + O2 → SO2 + O: rate = k[SO][O2]
c. 2CH3 → C2H6: rate = k[CH3]2
d. ClOO → Cl + O2: rate = k
5. Cleavage of C2H6 to produce two CH3· radicals is a gas-phase reaction that occurs at 700°C. This reaction is first order, with k = 5.46 × 10−4
s−1. How long will it take for the reaction to go to 15% completion? to 50% completion?
6. Three chemical processes occur at an altitude of approximately 100 km in Earth’s atmosphere.
k1
+ +
N + O2 −
→ N2 + O
2 2
k2
+ +
O +O−
→ O2 + O
2
k3
+ +
O + N2 −
→ NO +N

Write a rate law for each elementary reaction. If the rate law for the overall reaction were found to be rate = k[N2+][O2], which one of the steps is
rate limiting?
7. The oxidation of aqueous iodide by arsenic acid to give I3− and arsenous acid proceeds via the following reaction:
kf
− + −
H3 AsO4 (aq) + 3 I (aq) + 2 H (aq) ⇌ H3 AsO3 (aq) + I (aq) + H2 O(l)
3
kr

Write an expression for the initial rate of decrease of [I3−], Δ[I3−]/Δt. When the reaction rate of the forward reaction is equal to that of the reverse
reaction: kf/kr = [H3AsO3][I3−]/[H3AsO4][I−]3[H+]2. Based on this information, what can you say about the nature of the rate-determining steps for
the reverse and the forward reactions?

Answer

5. 298 s; 1270 s

Contributors
Anonymous

Transition State Theory

According to TST, between the state where molecules are reactants and the state where molecules are products, there is a state
known as the transition state. In the transition state, the reactants are combined in a species called the activated complex. The
theory suggests that there are three major factors that determine whether a reaction will occur:
1. The concentration of the activated complex
2. The rate at which the activated complex breaks apart
3. The way in which the activated complex breaks apart: whether it breaks apart to reform the reactants or whether it breaks apart
to form a new complex, the products.

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Collision theory proposes that not all reactants that combine undergo a reaction. However, assuming the stipulations of the collision
theory are met and a successful collision occurs between the molecules, transition state theory allows one of two outcomes: a return
to the reactants, or a rearranging of bonds to form the products.
Template:ExampleStart

The example reaction shown above involves the reactants, hydroxide and bromomethane, forming the products, methanol and
bromide. The first part of the image shows the reactants. The second part of the image shows the transition state, in which the
activated complex is formed, with rearranged molecules and different bonds. The dotted lines represent the transitory bonds that
form during this stage. The activated complex is clearly different than the reactants or the products. A successful collision and
reaction have clearly occurred because in the third part of the image products (methanol and bromide) are formed that are different
than the reactants (hydroxide and bromomethane).

Reaction Profiles
Using a reaction profile, the energy necessary to complete a reaction can be determined by plotting energy values on the y-axis of
a Cartesian plane. On the x-axis, the reaction progress is plotted. A graph such as the one below is the result:

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This graph illustrates where the molecules exist as reactants, products, or in the transition state. The relationship between potential
energy and reaction rate is clear. Also illustrated is the amount of energy required to initiate a reaction—the activation energy (Ea).
A reaction profile can also be used to find the enthalpy (ΔH) of the reaction, by subtracting the energy of the products from the
energy of the reactants. This example reaction is exothermic. The Gibbs energy change of the reaction (ΔG) is equal to the
activation energy of the forward reaction. The reaction profile for a two step reaction, shown below, displays all the activated
complexes that occur during the reaction , as well as any intermediates formed.

Applications
The main application of the transition state theory is in reactions catalyzed by enzymes. The introduction of an enzyme catalyst into
a reaction lowers the activation energy of that reaction. Research detailing enzymes' specific interactions with molecules, including
those in the transition state, has shown that the enzymes actually increase the stability of the activated complex in the transition
state. This is important in terms of enzyme activity such as the induced fit model and enzymes used in inhibitors. In more general
terms, however, the transition state theory is useful in determining a reaction will proceed. By knowing which transition states will
form, and what differing activation energies are, it is possible to map out the course of a reaction, and calculate quantities such as
the reaction rate and the rate constant.

Concept Questions
1. Which two values in the Arrhenius equation are explained by transition state theory?
2. Assuming a successful collision occurs, what two outcomes are possible for an activated complex?
3. What is a reaction profile? What two values does it compare? What values can it be used to determine?
4. Label the axes, reactants, products, transition state, Ea forward, Ea reverse, and ΔH for the blank reaction profile below.

5. For a hypothetical exothermic reaction, the Ea reverse=600kJ and the Ea forward=200kJ. What is the value of ΔH?

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6. In the reaction depicted below, how many activated complexes are present? How many intermediates? Is the first step
endothermic or exothermic? What about the reaction as a whole?

Answers
1. The pre-exponential factor (A) and the activation energy (Ea).
2. The activated complex can either reform the reactants, or form products.
3. A reaction profile is a graph that compares the potential energy of a reaction and the progression of the reaction. The activation
energy (Ea) and enthalpy (ΔH) can be determined from it.
4.

5. Ea reverse=Ea forward + |ΔH|. Thus, 600kJ=200kJ + |ΔH|. |ΔH|=400kJ. The reaction is exothermic, thus ΔH must be negative.
The answer is -400kJ.
6. There are two activated complexes, and one intermediate. The first step is endothermic; however, the overall reaction is
exothermic.

Outside Links
http://en.wikipedia.org/wiki/Transition_state_theory
http://video.google.com/videoplay?do...86132780827666
http://www.youtube.com/watch?v=2ae8aBoEwS8

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References
1. Gross, Dixie J., and Ralph H. Petrucci. General Chemistry Principles and Modern Applications, Ninth Editon : Study Guide.
Upper Saddle River: Prentice Hall PTR, 2006.
2. Pauling, Linus. General Chemistry. Minneapolis: Dover Publications, Incorporated, 1989.
3. Petrucci, Ralph H., William S. Harwood, and Geoff E. Herring. General Chemistry : Principles and Modern Applications.
Upper Saddle River: Prentice Hall PTR, 2006.
4. Barker, Brett. Peterson's Master AP Chemistry. Lawrenceville, NJ: Peterson's, a Nelnet company, 2007.

Further Reading
Kinetics and the Rate Equation

MasterOrganicChemistry
Part 12: Chemical Kinetics
What’s A Transition State?

Cliffs Notes
Kinetics and Rate

Slide Presentations
Reaction kinetics in organic chemistry
Web Pages
Transition State Theory and kinetics
Videos
Transition state theory lecture
7.4 Kinetics is shared under a CC BY-NC-SA 4.0 license and was authored, remixed, and/or curated by LibreTexts.

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7.5 Product Distributions
Quite frequently, chemical reactions produce more than one product. In such circumstances, we need to consider the product
distribution, the ratio of one product to another. How much of one product we get in relation to other products can be determined
from energetic considerations, but what energies one must consider depends on the type of reaction: reversible vs. irreversible.

Reversible Reactions
Because reversible reactions are in equilibrium, the ratio of potential products depends entirely on their relative energies (∆G°)
using the relationship ∆G° = -RTlnK. Algebraic rearrangement produces K = e-∆G°/RT and the equiibrium constant K is merely the
ratio of one product concentration to the other. Thus, the ratio of products in a reversible equilibrium depends only on the relative
energies of the competing products. The major product in a reversible reaction will be the more stable one.

Irreversible Reactions
Conversely, in an irreversible reaction, the ratio of products from competitive pathways is not dependent on the stabilities of the
various products because the reaction is not operating under equiibrium conditions. Instead, the ratio of products in an irreversible
sequence depends on the rates at which each product is produced. Algebraic manipulation of the rate equations gives us an
expression for the ratio of products that depends only on the ratio of rate constants. That ratio in turn depends on a difference in
the energies of the respective transition states. Thus, the product ratio of an irreversible reaction depends only on the difference in
energies between the two competing transition states leading to the different products.

Further Reading
Wikipedia - Kinetic vs. Thermodynamic Control
Youtube - Kinetic vs. Thermodynamic Control
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7.6 Hammond's Postulate
Now, back to transition states. Chemists are often very interested in trying to learn about what the transition state for a given
reaction looks like, but addressing this question requires an indirect approach because the transition state itself cannot be observed.
In order to gain some insight into what a particular transition state looks like, chemists often invoke the Hammond postulate,
which states that a transition state resembles the structure of the nearest stable species. For an exergonic reaction, therefore, the
transition state resembles the reactants more than it does the products.

If we consider a hypothetical exergonic reaction between compounds A and B to form AB, the distance between A and B would be
relatively large at the transition state, resembling the starting state where A and B are two isolated species. In the hypothetical
endergonic reaction between C and D to form CD, however, the bond formation process would be much further along at the TS
point, resembling the product.

The Hammond Postulate is a very simplistic idea, which relies on an assumption that potential energy surfaces are parabolic.
Although such an assumption is not rigorously true, it is fairly reliable and allows chemists to make energetic arguments about
transition states by employing arguments about the stability of a related species. Since the formation of a reactive intermediate is
very reliably endergonic, arguments about the stability of reactive intermediates can serve as proxy arguments about transition
state stability.

Further Reading

MasterOrganicChemistry
Hammond’s Postulate

Wikipedia
Hammond's Postulate

Book Sections
Hammond’s Postulate

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7.6 Hammond's Postulate is shared under a CC BY-NC-SA 4.0 license and was authored, remixed, and/or curated by LibreTexts.

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 CHAPTER OVERVIEW

Chapter 8. Acid-Base Reactions

Purdue CHM 26505: Organic

Chemistry for Chemistry Majors (1st
Semester)
Fall 2014: Prof. Mark Lipton

Template:HideTOC

Topic hierarchy
8.1 Brønsted Acidity and Basicity
8.2 Factors Affecting Brønsted Acidity
8.3: pKa Values
8.4 Solvent Effects

Chapter 8. Acid-Base Reactions is shared under a CC BY-NC-SA 4.0 license and was authored, remixed, and/or curated by LibreTexts.

1
8.1 Brønsted Acidity and Basicity
In 1923, chemists Johannes Nicolaus Brønsted and Thomas Martin Lowry independently developed definitions of acids and bases
based on the compounds' abilities to either donate or accept protons (H ions). In this theory, acids are defined as proton donors;
+

whereas bases are defined as proton acceptors. A compound that acts as both a Brønsted-Lowry acid and base together is called
amphoteric.

The Brønsted-Lowry Theory of Acids and Bases

Brønsted-Lowry theory of acid and bases took the Arrhenius definition one step further, as a substance no longer needed to be
composed of hydrogen (H+) or hydroxide (OH-) ions in order to be classified as an acid or base. For example , consider the
following chemical equation:
+ −
H C l (aq) + N H3 (aq) → N H (aq) + C l (aq) (1)
4

Here, hydrochloric acid (HCl) "donates" a proton (H+) to ammonia (NH3) which "accepts" it , forming a positively charged
ammonium ion (NH4+) and a negatively charged chloride ion (Cl-). Therefore, HCl is a Brønsted-Lowry acid (donates a proton)
while the ammonia is a Brønsted-Lowry base (accepts a proton). Also, Cl- is called the conjugate base of the acid HCl and NH4+ is
called the conjugate acid of the base NH3.
A Brønsted-Lowry acid is a proton (hydrogen ion) donor.
A Brønsted-Lowry base is a proton (hydrogen ion) acceptor.
In this theory, an acid is a substance that can release a proton (like in the Arrhenius theory) and a base is a substance that can
accept a proton. A basic salt, such as Na+F-, generates OH- ions in water by taking protons from water itself (to make HF):
− −
F + H2 O(l) ⇌ H F(aq) + OH (2)
(aq)

When a Brønsted acid dissociates, it increases the concentration of hydrogen ions in the solution, [H +
; conversely, Brønsted bases
]

dissociate by taking a proton from the solvent (water) to generate [OH ]. −

Acid dissociation
− +
H A(aq) ⇌ A +H (3)
(aq) (aq)

Acid Ionization Constant:

− +
[A ][ H ]
Ka = (4)
[H A]

Base dissociation:
+ −
B(aq) + H2 O(l) ⇌ H B + OH (5)
(aq) (aq)

Base Ionization Constant

+ −
[H B ][OH ]
Kb = (6)
[B]

The determination of a substance as a Brønsted-Lowery acid or base can only be done by observing the reaction. In the case of the
HOH it is a base in the first case and an acid in the second case.

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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 that substance is the acid (donates hydrogen ions). If the number of hydrogens has increased
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 conjugate
acid and conjugate base compared to those on the left. Also note that the original acid turns in the conjugate base after the reaction
is over.

 Note

Acids are Proton Donors and Bases are Proton Acceptors

For a reaction to be in equilibrium a transfer of electrons needs to occur. The acid will give an electron away and the base will
receive the electron. Acids and Bases that work together in this fashion are called a conjugate pair made up of conjugate acids and
conjugate bases.
− +
HA + Z ⇌ A + HZ (7)

A stands for an Acidic compound and Z stands for a Basic compound

A Donates H to form HZ+.
Z Accepts H from A which forms HZ+
A- becomes conjugate base of HA and in the reverse reaction it accepts a H from HZ to recreate HA in order to remain in
equilibrium
HZ+ becomes a conjugate acid of Z and in the reverse reaction it donates a H to A- recreating Z in order to remain in
equilibrium

Questions
1. Why is H A an Acid?
2. Why is Z a Base?
−

3. How can A- be a base when HA was and Acid?

4. How can HZ+ be an acid when Z used to be a Base?
5. Now that we understand the concept, let's look at an an example with actual compounds!
+ ¯
H C l + H2 O ⇌ H3 O + Cl (8)

HCL is the acid because it is donating a proton to H2O

H2O is the base because H2O is accepting a proton from HCL
H3O+ is the conjugate acid because it is donating an acid to CL turn into it's conjugate acid H2O
Cl¯ is the conjugate base because it accepts an H from H3O to return to it's conjugate acid HCl
How can H2O be a base? I thought it was neutral?

Answers
1. It has a proton that can be transferred
2. It receives a proton from HA

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 3. A- is a conjugate base because it is in need of a H in order to remain in equilibrium and return to HA
4. HZ+ is a conjugate acid because it needs to donate or give away its proton in order to return to it's previous state of Z
5. In the Brønsted-Lowry Theory what makes a compound an element or a base is whether or not it donates or accepts protons. If
the H2O was in a different problem and was instead donating an H rather than accepting an H it would be an acid!

Contributors and Attributions

Sarah Rundle (UCD), Charles Ophardt, Professor Emeritus, Elmhurst College; Virtual Chembook

Further Reading

MasterOrganicChemistry
Introducing Acids and Bases
Walkthrough of Acid-Base Reactions: Acidity
Walkthrough of Acid-Base Reactions: Basicity

Websites
Wikipedia - Brønsted-Lowry Acid-Base Theory
Brønsted-Lowry Concept
The Acid-Base Theory of Brønsted and Lowry
8.1 Brønsted Acidity and Basicity is shared under a CC BY-NC-SA 4.0 license and was authored, remixed, and/or curated by LibreTexts.
Brønsted Concept of Acids and Bases is licensed CC BY-NC-SA 4.0.

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8.2 Factors Affecting Brønsted Acidity
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:

A hydroxonium ion is formed together with the anion (negative ion) from the acid.
This equilibrium is sometimes simplified by leaving out the water to emphasise the ionisation of the acid.

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 ionisation is very incomplete. At any one time, most of the acid will be present in
the solution as un-ionised molecules. For example, in the case of dilute ethanoic acid, the solution contains about 99% of ethanoic
acid molecules - at any instant, only about 1% have actually ionised. The position of equilibrium therefore lies well to the left.

Comparing the strengths of weak acids

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

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

Why are these acids acidic?

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

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

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

 Example 1 : Ethanoic Acid

Ethanoic acid has the structure:

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

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

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

All the oxygen lone pairs have been left out of this diagram to avoid confusion. Because the oxygens are more electronegative
than the carbon, the delocalised system is heavily distorted so that the electrons spend much more time in the region of the
oxygen atoms.
So where is the negative charge in all this? It has been spread around over the whole of the -COO- group, but with the greatest
chance of finding it in the region of the two oxygen atoms. Ethanoate ions can be drawn simply as:

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

 Example 2 : Phenol

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

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

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

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

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

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

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

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

 Example 3 : Ethanol

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

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

Variations in acid strengths between different carboxylic acids

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

pKa

HCOOH 3.75

CH3COOH 4.76

CH3CH2COOH 4.87

CH3CH2CH2COOH 4.82

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

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

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

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

pKa

CH3COOH 4.76

CH2ClCOOH 2.86

CHCl2COOH 1.29

CCl3COOH 0.65

Trichloroethanoic acid is quite a strong acid.

Attaching different halogens also makes a difference. Fluorine is the most electronegative and so you would expect it to be most
successful at pulling charge away from the -COO- end and so strengthening the acid.

pKa

CH2FCOOH 2.66

CH2ClCOOH 2.86

CH2BrCOOH 2.90

CH2ICOOH 3.17

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

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

pKa

CH3CH2CH2COOH 4.82

CH3CH2CHClCOOH 2.84

CH3CHClCH2COOH 4.06

CH2ClCH2CH2COOH 4.52

The chlorine is effective at withdrawing charge when it is next-door to the -COO- group, and much less so as it gets even one
carbon further away.

Further Reading

MasterOrganicChemistry
Acidity Trends
5 Key Factors Affecting Acidity

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Carey 4th Edition Online
Acidity and Basicity

Websites
Factors Affecting Brønsted-Lowry Acidity
8.2 Factors Affecting Brønsted Acidity is shared under a CC BY-NC-SA 4.0 license and was authored, remixed, and/or curated by LibreTexts.
Organic Acids by Jim Clark is licensed CC BY-NC 4.0.

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8.3: pKa Values
It is helpful to have a way of comparing Bronsted-Lowry acidities of different compounds. If the chemistry of protons involves
being passed from a more acidic site to a less acidic site, then the site that binds the proton more tightly will retain the proton, and
the site that binds protons less tightly will lose the proton. If we know which sites bind protons more tightly, we can predict in
which direction a proton will be transferred.

Figure AB9.1. In which direction will the equilibrium lie? Which base gets the proton?
There is an experimentally-determined parameter that tells us how tightly protons are bound to different compounds.
"Experimental" often implies to students "untested" or "unreliable", but here it means that someone has done the work to measure
how tightly the proton is bound. Experimental in this sense means "based on physical evidence".
This experimental parameter is called "the pKa". The pKa measures how tightly a proton is held by a Bronsted acid. A pKa may be
a small, negative number, such as -3 or -5. It may be a larger, positive number, such as 30 or 50. The lower the pKa of a Bronsted
acid, the more easily it gives up its proton. The higher the pKa of a Bronsted acid, the more tightly the proton is held, and the less
easily the proton is given up.

Figure AB9.2. The pKa scale as an index of proton availability.

Low pKa means a proton is not held tightly.
pKa can sometimes be so low that it is a negative number!
High pKa means a proton is held tightly.

Figure AB9.3. Some Bronsted acidic compounds; these compounds all supply protons relatively easily.
For example, nitric acid and hydrochloric acid both give up their protons very easily. Nitric acid in water has a pKa of -1.3 and
hydrobromic acid has a pKa of -9.0. On the other hand, acetic acid (found in vinegar) and formic acid (the irritant in ant and bee
stings) will also give up protons, but hold them a little more tightly. Their pKas are reported as 4.76 and 3.77, respectively. Water
does not give up a proton very easily; it has a pKa of 15.7. Methane is not really an acid at all, and it has an estimated pKa of about
50.

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 Figure AB9.4. Some not-so-acidic compounds. Water is very, very weakly acidic; methane is not really acidic at all.
The pKa measures the "strength" of a Bronsted acid. A proton, H+, is a strong Lewis acid; it attracts electron pairs very effectively,
so much so that it is almost always attached to an electron donor. A strong Bronsted acid is a compound that gives up its proton
very easily.
A weak Bronsted acid is one that gives up its proton with more difficulty. Going to a farther extreme, a compound from which it is
very, very difficult to remove a proton is not considered to be an acid at all.
When a compound gives up a proton, it retains the electron pair that it formerly shared with the proton. It becomes a conjugate
base. Looked at another way, a strong Bronsted acid gives up a proton easily, becoming a weak Bronsted base. The Bronsted base
does not easily form a bond to the proton. It is not good at donating its electron pair to a proton. It does so only weakly.
In a similar way, if a compound gives up a proton and becomes a strong base, the base will readily take the proton back again.
Effectively, the strong base competes so well for the proton that the compound remains protonated. The compound remains a
Bronsted acid rather than ionizing and becoming the strong conjugate base. It is a weak Bronsted acid.

Figure AB9.5. The pKa scale and its effect on conjugate bases.
"Strong" Bronsted acids ionize easily to provide H+.
This term is usually used to describe common acids such as sulfuric acid and hydrobromic acid.
"Weak" Bronsted acids do not ionize as easily.
This term is often used to describe common acids such as acetic acid and hydrofluoric acid.
However, the terms "strong" and "weak" are really relative. pKa values that we have seen range from -5 to 50. If something with a
pKa of 4 is described as a weak acid, what is something with a pKa of 25? A very, very weak acid? It is certainly a better source of
protons than something with a pKa of 35. Is that a very, very, very, very weak acid? How many "verys" are there in a pKa unit?
This idea is also true when considering the opposite: a base picking up a proton to form a conjugate acid. How tightly that
conjugate acid holds a proton is related to how strongly the base can remove protons from other acids. The weaker something is as
a source of protons, the stronger its conjugate is as a proton sponge.

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 Figure AB9.6. Examples of a strong base and an even stronger one.
Be careful. The terms "strong acid" and "weak acid" can be used relatively, rather than absolutely.
The same is true for "strong base" and "weak base".
Sometimes, whether something is called "strong" or "weak" depends on what else it is being compared to.

Problem AB9.1.
Find a pKa table. Use it to help you decide which of the following pairs is the most Bronsted acidic in water.
a) HNO3 or HNO2 b) H2Se or H2O c) HCl or H2SO4 d) Be(OH)2 or HSeO3

Problem AB9.2.
Find a pKa table. Use it to help you decide which of the compounds in each pair forms the most basic conjugate after deprotonation
in water.
a) NH4+ or NH3 b) HCN or HSCN c) NH3 or H2O

Contributors
Chris P Schaller, Ph.D., (College of Saint Benedict / Saint John's University)

Further Reading

MasterOrganicChemistry
Acid-Base Reactions 4 – pKa
Acid-Base Reactions 5 – How to Use a pKa Table
The pKa Table is Your Friend

Khan Academy
Ka and pKa Derivation

Websites
Wikipedia - Acid Dissociation Constants
Acidity, Basicity and pKa (PDF)
8.3: pKa Values is shared under a CC BY-NC-SA 4.0 license and was authored, remixed, and/or curated by LibreTexts.

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8.4 Solvent Effects
Leveling effect
From Wikipedia, the free encyclopedia

Acid-base discrimination windows of common solvents[1]

Leveling effect or solvent leveling refers to the effect of solvent on the properties of acids and bases. The strength of a strong acid
is limited ("leveled") by the basicity of the solvent. Similarly the strength of a strong base is leveled by the acidity of the solvent.
When a strong acid is dissolved in water, it reacts with it to form hydronium ion (H3O+).[2] An example of this would be the
following reaction, where "HA" is the strong acid:

HA + H2O → A- + H3O+

Any acid that is stronger than H3O+ reacts with H2O to form H3O+. Therefore, no acid stronger than H3O+ exists in H2O. Similarly,
when ammonia is the solvent, the strongest acid is ammonium (NH4+), thus HCl and a super acid exert the same acidifying effect.
The same argument applies to bases. In water, OH- is the strongest base. Thus, even though sodium amide (NaNH2) is an
exceptional base (pKa of NH3 ~ 33), in water it is only as good as sodium hydroxide. On the other hand, NaNH2 is a far more basic
reagent in ammonia than is NaOH.
The pH range allowed by a particular solvent is called the acid-base discrimination window.[1]

Leveling and differentiating solvents

In a differentiating solvent, various acids dissociate to different degrees and thus have different strengths. In a leveling solvent,
several acids are completely dissociated and are thus of the same strength. A weakly basic solvent has less tendency than a strongly
basic one to accept a proton. Similarly a weak acid has less tendency to donate protons than a strong acid. As a result a strong acid
such as perchloric acid exhibits more strongly acidic properties than a weak acid such as acetic acid when dissolved in a weakly
basic solvent. On the other hand, all acids tend to become indistinguishable in strength when dissolved in strongly basic solvents
owing to the greater affinity of strong bases for protons. This is called the leveling effect. Strong bases are leveling solvents for
acids, weak bases are differentiating solvents for acids. Because of the leveling effect of common solvents, studies on super acids
are conducted in solvents that are very weakly basic such as sulfur dioxide (liquefied) and SO2ClF.[3]
Types of solvent on the basis of proton interaction On the basis of proton interaction, solvents are of four types,
(i) Protophilic solvents: Solvents which have greater tendency to accept protons, i.e., water, alcohol, liquid ammonia, etc.
(ii) Protogenic solvents: Solvents which have the tendency to produce protons, i.e., water, liquid hydrogen chloride, glacial acetic
acid, etc.
(iii) Amphiprotic solvents: Solvents which act both as protophilic or protogenic, e.g., water, ammonia, ethyl alcohol, etc.
(iv) Aprotic solvents: Solvents which neither donate nor accept protons, e.g., benzene, carbon tetrachloride, carbon disulphide, etc.
HCl acts as an acid in H2O, a stronger acid in NH3, a weak acid in CH3COOH, neutral in C6H6 and a weak base in HF.

References
1. Atkins, P.W. (2010). Shriver and Atkins' Inorganic Chemistry, Fifth Edition. Oxford University Press. p. 121. ISBN 978-1-42-
921820-7.

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 2. Zumdahl, S. S. “Chemistry” Heath, 1986: Lexington, MA. ISBN 0-669--04529-2.
3. Olah, G. A.; Prakash, G. K. S.; Wang, Q.; Li, X. (2001). "Hydrogen Fluoride–Antimony(V) Fluoride". In Paquette, L.
Encyclopedia of Reagents for Organic Synthesis. New York: J. Wiley & Sons. doi:10.1002/047084289X.rh037m.

8.4 Solvent Effects is shared under a CC BY-SA 4.0 license and was authored, remixed, and/or curated by LibreTexts.

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 CHAPTER OVERVIEW

Chapter 9. Isomerization Reactions

Purdue CHM 26505: Organic

Chemistry for Chemistry Majors (1st
Semester)
Fall 2014: Prof. Mark Lipton

Template:HideTOC

Topic hierarchy
9.1: Keto-Enol Tautomerization
9.2: 1,2-Shifts in Carbocations

Chapter 9. Isomerization Reactions is shared under a CC BY-NC-SA 4.0 license and was authored, remixed, and/or curated by LibreTexts.

1
9.1: Keto-Enol Tautomerization
For alkylation reactions of enolate anions to be useful, these intermediates must be generated in high concentration in the absence
of other strong nucleophiles and bases. The aqueous base conditions used for the aldol condensation are not suitable because the
enolate anions of simple carbonyl compounds are formed in very low concentration, and hydroxide or alkoxide bases induce
competing SN2 and E2 reactions of alkyl halides. It is necessary, therefore, to achieve complete conversion of aldehyde or ketone
reactants to their enolate conjugate bases by treatment with a very strong base (pKa > 25) in a non-hydroxylic solvent before any
alkyl halides are added to the reaction system. Some bases that have been used for enolate anion formation are: NaH (sodium
hydride, pKa > 45), NaNH2 (sodium amide, pKa = 34), and LiN[CH(CH3)2]2 (lithium diisopropylamide, LDA, pKa 36). Ether
solvents like tetrahydrofuran (THF) are commonly used for enolate anion formation. With the exception of sodium hydride and
sodium amide, most of these bases are soluble in THF. Certain other strong bases, such as alkyl lithium and Grignard reagents,
cannot be used to make enolate anions because they rapidly and irreversibly add to carbonyl groups. Nevertheless, these very
strong bases are useful in making soluble amide bases. In the preparation of lithium diisopropylamide (LDA), for example, the only
other product is the gaseous alkane butane.

Because of its solubility in THF, LDA is a widely used base for enolate anion formation. In this application, one equivalent of
diisopropylamine is produced along with the lithium enolate, but this normally does not interfere with the enolate reactions and is
easily removed from the products by washing with aqueous acid. Although the reaction of carbonyl compounds with sodium
hydride is heterogeneous and slow, sodium enolates are formed with the loss of hydrogen, and no other organic compounds are
produced.
Examples

If the formed enolate is stabilized by more than one carbonyl it is possible to use a weaker base such as sodium ethoxide.
NaOCH2CH3 = Na+ -OCH2CH3 = NaOEt

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Because of the acidity of α hydrogens, carbonyls undergo keto-enol tautomerism. Tautomers are rapidly interconverted
constitutional isomers, usually distinguished by a different bonding location for a labile hydrogen atom and a differently located
double bond. The equilibrium between tautomers is not only rapid under normal conditions, but it often strongly favors one of the
isomers (acetone, for example, is 99.999% keto tautomer). Even in such one-sided equilibria, evidence for the presence of the
minor tautomer comes from the chemical behavior of the compound. Tautomeric equilibria are catalyzed by traces of acids or bases
that are generally present in most chemical samples.

However under acidic and basic conditions the equilibrium can be shifted to the right

Mechanism for Enol Formation

Acid conditions
1) Protonation of the Carbonyl

2) Enol formation

Basic conditions
1) Enolate formation

2) Protonation

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Contributors
William Reusch, Professor Emeritus (Michigan State U.), Virtual Textbook of Organic Chemistry
Prof. Steven Farmer (Sonoma State University)

Further Reading

Wikipedia
Keto-enol tautomerism

Khan Academy
Keto-enol tautomerism
MasterOrganicChemistry
Keto-enol tautomerism
9.1: Keto-Enol Tautomerization is shared under a CC BY-NC-SA 4.0 license and was authored, remixed, and/or curated by LibreTexts.
Synthesis of Enols and Enolates is licensed CC BY-NC-SA 4.0.

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9.2: 1,2-Shifts in Carbocations
Carbocation rearrangements are extremely common in organic chemistry reactions are are defined as the movement of a
carbocation from an unstable state to a more stable state through the use of various structural reorganizational "shifts" within the
molecule. Once the carbocation has shifted over to a different carbon, we can say that there is a structural isomer of the initial
molecule. However, this phenomenon is not as simple as it sounds.

Introduction
Whenever alcohols are subject to transformation into various carbocations, the carbocations are subject to a phenomenon known as
carbocation rearrangement. A carbocation, in brief, holds the positive charge in the molecule that is attached to three other groups
and bears a sextet rather than an octet. However, we do see carbocation rearrangements in reactions that do not contain alcohol as
well. Those, on the other hand, require more difficult explanations than the two listed below. There are two types of
rearrangements: hydride shift and alkyl shift. These rearrangements usualy occur in many types of carbocations. Once rearranged,
the molecules can also undergo further unimolecular substitution (SN1) or unimolecular elimination (E1). Though, most of the time
we see either a simple or complex mixture of products. We can expect two products before undergoing carbocation rearrangement,
but once undergoing this phenomenon, we see the major product.

Hydride Shift
Whenever a nucleophile attacks some molecules, we typically see two products. However, in most cases, we normally see both a
major product and a minor product. The major product is typically the rearranged product that is more substituted (aka more
stable). The minor product, in contract, is typically the normal product that is less substituted (aka less stable).
The reaction: We see that the formed carbocations can undergo rearrangements called hydride shift. This means that the two
electron hydrogen from the unimolecular substitution moves over to the neighboring carbon. We see the phenomenon of hydride
shift typically with the reaction of an alcohol and hydrogen halides, which include HBr, HCl, and HI. HF is typically not used
because of its instability and its fast reactivity rate. Below is an example of a reaction between an alcohol and hydrogen chloride:

GREEN (Cl) = nucleophile BLUE (OH) = leaving group ORANGE (H) = hydride shift proton RED(H) = remaining proton
The alcohol portion (-OH) has been substituted with the nucleophilic Cl atom. However, it is not a direct substitution of the OH
atom as seen in SN2 reactions. In this SN1 reaction, we see that the leaving group, -OH, forms a carbocation on Carbon #3 after
receiving a proton from the nucleophile to produce an alkyloxonium ion. Before the Cl atom attacks, the hydrogen atom attached to
the Carbon atom directly adjacent to the original Carbon (preferably the more stable Carbon), Carbon #2, can undergo hydride
shift. The hydrogen and the carbocation formally switch positions. The Cl atom can now attack the carbocation, in which it forms
the more stable structure because of hyperconjugation. The carbocation, in this case, is most stable because it attaches to the
tertiary carbon (being attached to 3 different carbons). However, we can still see small amounts of the minor, unstable product. The
mechanism for hydride shift occurs in multiple steps that includes various intermediates and transition states. Below is the
mechanism for the given reaction above:

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Hydration of Alkenes: Hydride Shift
In a more complex case, when alkenes undergo hydration, we also observe hydride shift. Below is the reaction of 3-methyl-1-
butene with H3O+ that furnishes to make 2-methyl-2-butanol:

Once again, we see multiple products. In this case, however, we see two minor products and one major product. We observe the
major product because the -OH substitutent is attached to the more substituted carbon. When the reactant undergoes hydration, the
proton attaches to carbon #2. The carbocation is therefore on carbon #2. Hydride shift now occurs when the hydrogen on the
adjacent carbon formally switch places with the carbocation. The carbocation is now ready to be attacked by H2O to furnish an
alkyloxonium ion because of stability and hyperconjugation. The final step can be observed by another water molecule attacking
the proton on the alkyloxonium ion to furnish an alcohol. We see this mechanism below:

Alkyl Shift
Not all carbocations have suitable hydrogen atoms (either secondary or tertiary) that are on adjacent carbon atoms available for
rearrangement. In this case, the reaction can undergo a different mode of rearrangement known as alkyl shift (or alkyl group

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migration). Alkyl Shift acts very similarily to that of hydride shift. Instead of the proton (H) that shifts with the nucleophile, we see
an alkyl group that shifts with the nucleophile instead. The shifting group carries its electron pair with it to furnish a bond to the
neighboring or adjacent carbocation. The shifted alkyl group and the positive charge of the carbocation switch positions on the
moleculeReactions of tertiary carbocations react much faster than that of secondary carbocations. We see alkyl shift from a
secondary carbocation to tertiary carbocation in SN1 reactions:

We observe slight variations and differences between the two reactions. In reaction #1, we see that we have a secondary substrate.
This undergoes alkyl shift because it does not have a suitable hydrogen on the adjacent carbon. Once again, the reaction is similar
to hydride shift. The only difference is that we shift an alkyl group rather than shift a proton, while still undergoing various
intermediate steps to furnish its final product.
With reaction #2, on the other hand, we can say that it undergoes a concerted mechanism. In short, this means that everything
happens in one step. This is because primary carbocations cannot be an intermediate and they are relatively difficult processes
since they require higher temperatures and longer reaction times. After protonating the alcohol substrate to form the alkyloxonium
ion, the water must leave at the same time as the alkyl group shifts from the adjacent carbon to skip the formation of the unstable
primary carbocation.

Carbocation Rearrangements for E1 Reactions

E1 reactions are also affected by alkyl shift. Once again, we can see both minor and major products. However, we see that the more
substituted carbons undergo the effects of E1 reactions and furnish a double bond. See practice problem #4 below for an example
as the properties and effects of carbocation rearrangements in E1 reactions are similar to that of alkyl shifts.

1,3-Hydride and Greater Shifts

Typically, hydride shifts can occur at low temperatures. However, by heating the solutionf of a cation, it can easily and readily
speed the process of rearrangement. One way to account for a slight barrier is to propose a 1,3-hydride shift interchanging the

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functionality of two different kinds of methyls. Another possibility is 1,2 hydride shift in which you could yield a secondary
carbocation intermediate. Then, a further 1,2 hydride shift would give the more stable rearranged tertiary cation.
More distant hydride shifts have been observed, such as 1,4 and 1,5 hydride shifts, but these arrangements are too fast to undergo
secondary cation intermediates.

Analogy
Carbocation rearrangements happen very readily and often occur in many organic chemistry reactions. Yet, we typically neglect
this step. Dr. Sarah Lievens, a Chemistry professor at the University of California, Davis once said carbocation rearrangements can
be observed with various analogies to help her students remember this phenomenon. For hydride shifts: "The new friend
(nucleophile) just joined a group (the organic molecule). Because he is new, he only made two new friends. However, the popular
kid (the hydrogen) glady gave up his friends to the new friend so that he could have even more friends. Therefore, everyone won't
be as lonely and we can all be friends." This analogy works for alkyl shifts in conjunction with hydride shift as well.

References
1. Vogel, Pierre. Carbocation Chemistry. Amsterdam: Elsevier Science Publishers B.V., 1985.
2. Olah, George A. and Prakash, G.K. Surya. Carbocation Chemistry. New Jersey: John Wiley & Sons, Inc., 2004.
3. Vollhardt, K. Peter C. and Schore, Neil E. Organic Chemistry: Structure and Function. New York: Bleyer, Brennan, 2007.

Outside links
http://en.Wikipedia.org/wiki/Carboca..._rearrangement
Watch a short presentation on the carbocation rearrangement phenomenon

Problems

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Answers to Practice Problems

Contributors
Jeffrey Ma

Further Reading

MasterOrganicChemistry
1,2-Hydride Shifts
1,2-Alkyl Shifts

Khan Academy
Carbocation Shifts

9.2.5 https://chem.libretexts.org/@go/page/41021
Leah4Sci
1,2- Shifts

Web Pages
Wagner-Meerwein Rearrangement

Videos
Carbocation Rearrangements
9.2: 1,2-Shifts in Carbocations is shared under a CC BY-NC-SA 4.0 license and was authored, remixed, and/or curated by LibreTexts.
Carbocation Rearrangements is licensed CC BY-NC-SA 4.0.

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Course Content
I. Chemical Bonding and Electronic Structure
A. Electronic configuration and valence
1. Aufbau principle
2. Valence shell and core shells
3. Noble gas configuration and 8 electron rule
B. Covalent vs ionic bonding
1. Definition of terms
2. Electron count in covalent bonds
3. Multiple covalent bonds
C. Atomic orbitals and hybridization
1. VSEPR principle and bonding geometry
2. Tetrahedral geometry and atomic orbitals
3. Hybridization of atomic orbitals
4. sp3, sp2 and sp hybridization of carbon
5. inclusion of lone pairs in VSEPR model
D. Sigma and π bonding
E. Electronegativity and polarization of covalent bonds
F. Resonance
G. Formal charge, hypovalency and hypervalency
H. Conjugation of π electrons
I. Aromaticity

II. Functional groups and Nomenclature

A. Hydrocarbons
1. Alkanes
2. Cycloalkanes
3. Alkenes, dienes and polyenes
4. Alkynes
5. Arenes
B. Haloalkanes
C. Ethers, Sulfides and Epoxides
D. Amines
E. Alcohols
F. Carbonyls
1. Aldehydes
2. Ketones
G. Carboxylic acids
H. Carboxylic acid derivatives
1. Esters
2. Amides
3. Acid Halides
4. Anhydrides
5. Nitriles
6. Imides
I. Esters of inorganic acids: phosphates, sulfates, nitrates
J. IUPAC rules for nomenclature
1. Hydrocarbon rules

1
 2. Unsaturation
3. Functional group prioritization
4. Suffixes and substituent names for functional groups

III. Stereochemistry
A. Definition of terms: stereoisomer, chirality, conformation, configuration
B. Conformational isomerism
1. alkanes
2. cyclohexane
3. substituted cyclohexane
C. Molecular chirality and optical activity
D. Configurational isomerism
1. Stereogenic carbon and the Cahn-Ingold-Prelog system
2. Enantiomers and diastereomers
3. E and Z alkenes
4. cis- and trans- disubstituted cycloalkanes
5. Stereogenicity in atoms other than carbon

IV. Intermolecular interactions and physical properties

A. Boiling point and melting point
1. Effect of molecular weight
2. Polarity and dipole-dipole interactions
3. Hydrogen bonding interactions and their effect
B. Solubility
1. Solvent-solute interactions
2. Dipole-dipole
3. Hydrogen bonding
4. The hydrophobic effect
C. Chromatography
1. Exploitation of intermolecular interactions
2. Common stationary phases: silica and alumina
3. forms: TLC, column, HPLC and size exclusion

V. Reactive intermediates: carbocations, carbanions, free radicals

A. Carbocations
1. Trivalent carbon
2. Lack of an octet
3. sp2 hydridization
4. empty p orbital
5. Stability trends
6. Resonance stabilization
a. By neighboring π electrons
b. By neighboring heteroatoms with lone pairs
B. Carbanions
1. Lone pair on carbon
2. Retention of geometry
3. Configurational lability
4. Stability trends
C. Free radicals
1. Lack of an octet on C

2
 2. Neutrality of free radicals
3. Stability trends

VI. Spectroscopy
A. Infrared
1. Theory
2. Symmetry, dipole moments and intensity
3. Characteristic stretching frequencies
4. Bending and other vibrational motion
B. Mass spectrometry
1. Theory
2. Ionization methods
3. Fragmentation reactions
a. alpha cleavage
b. beta cleavage
c. McLafferty rearrangement
d. Isotoπc distribution
C. NMR
1. Theory
2. Chemical shift, deshielding and electronegativity
3. Diamagnetic anisotropy
4. Vicinal coupling
a. Idea
b. Coupling constant
c. Multiplicity (N+1 rule)
d. Effects of geometry on coupling constant
5. Geminal and 4-bond coupling
6. 13C NMR
7. Other nuclei (15N, 31P, 19F)
D. Integrated spectroscopy problems

VII. Reactivity and the movement of electrons

A. Lewis acids and bases; nucleophiles and electrophiles
B. Definition of terms: addition, elimination, substitution
C. Donation of electrons toward covalent bond
D. Use of curved arrow formalism to describe electron movement
1. Starts at reactive lone pair (or bond)
2. Terminates at midpoint of forming bond
3. Alternatively, ends at atom if changing charge state
E. Curved arrows in resonance
F. Kinetics and Thermodynamics
1. Reversibility and irreversibility
2. Le Chatelier’s Principle
3. Kinetics and transition state energies
4. Hammond’s postulate and the use of intermediates

VIII. Acid-Base Reactivity

A. Lewis acidity/basicity vs. Brønsted acidity/basicity
B. Factors affecting Brønsted acidity
1. Electronegativity

3
 2. Bond strength to hydrogen
3. Inductive effects
4. Resonance effects
5. Solvent effects
C. Quantifying acidity: pKa values
D. Representative pKa values of various functional groups
E. Solvents and the leveling effect

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4
I. Chemical Bonding and Electronic Structure

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II. Functional groups and Nomenclature

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III. Stereochemistry

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IV. Intermolecular interactions and physical properties

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V. Reactive intermediates: carbocations, carbanions, free radicals

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VI. Spectroscopy

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VII. Reactivity and the movement of electrons

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VIII. Acid-Base Reactivity

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Index
L
Leveling Effect
8.4 Solvent Effects
Glossary
Sample Word 1 | Sample Definition 1
Detailed Licensing
Overview
Title: Chem 26505: Organic Chemistry I (Lipton)
Webpages: 86
Applicable Restrictions: Noncommercial
All licenses found:
CC BY-NC-SA 4.0: 87.2% (75 pages)
Undeclared: 11.6% (10 pages)
CC BY-SA 4.0: 1.2% (1 page)

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Front Matter - Undeclared 2.9: Carboxylic Acids - CC BY-NC-SA 4.0
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Licensing - Undeclared Appendix - IUPAC Nomenclature Rules - CC BY-NC-
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Chapter 3. Stereochemistry - CC BY-NC-SA 4.0
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