Chemistry 140A Winter 2014 (K.

Albizati)
Chapter 2 Structure and Reactivity; Alkanes
Chemical Thermodynamics concerns the energy changes in chemical reactions; determines the extent to which a reaction will go to completion
Chemical Kinetics concerns the rate (speed) at which chemical reactions occur

Thermodynamics
-

All chemical reactions are reversible

Reactants and products interconvert to varying degrees depending on their structure

Consider a typical chemical reaction

A + B

C + D
[C] [D]

Keq =

[A] [B]
Keq is directly related to the Gibbs Standard Free Energy change via

Go =- RTlnKeq

generally expressed in kcal/mole

If Keq = 0.01 Go = +2.7 kcal/mole

If Keq = 1 Go = 0
If Keq = 10,000

Go = - 5.5

So.the extent to which a reaction occurs is dependent on Go

Go is directly related to the bond strengths involved in the chemical reaction as well as the energy dispersal of the system
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Chemistry 140A Winter 2014 (K. Albizati)

Put another way
Go = Ho - TSo

Ho is the enthalpy change or heat of reaction and is related mainly to changes in bond strengths in going from Reactants to products
So is the entropy change or degree of disorder of a system; this is more difficult to quantify but in general if one reactant molecule gives rise to 2
product molecules the entropy change is positive leading to a negative contribution to Go and therefore is thermodynamically favorable. The
converse is true

A
A + B

C + D

entropically favorable

entropically unfavorable

Kinetics
Basically, how fast does a system reach chemical equilibrium?
Dependent on the activation energy of a chemical reaction
Consider Paper.paper is unstable with respect to its combustion products CO2 and water:

PAPER + O2

CO2

H2O

large negative Go

Yet it happens so slowly at room temperature so as to be unobservable on our time frame. This is because the activation energy is so high.
This can be visualized with a potential energy diagram:

Chemistry 140A Winter 2014 (K. Albizati)

Where does the energy come from to get over the barrier?
From collisions between molecules. Collisions transfer energy between molecules. If heat is applied to molecules their kinetic energy increases
(they move faster) and hence the collision speed and rate increases. This can provide the energy needed to climb the barrier.

Arrhenius Equation
Consider

A + B

Reaction Rate = k[A] [B] in units of mol per liter per sec
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Chemistry 140A Winter 2014 (K. Albizati)

k = the rate constant and is
k = Ae Ea/RT
So.if the temperature of a reaction is increased, the rate of the reaction increases. This makes sense because as you raise the temperature of
molecules you raise their kinetic energy. A is the Arrhenius constant and each reaction has its own peculiar value of A.

An additional factor can influence the rate of a chemical reaction --- the concentration of the reactants
Take a look at the rate law again:

A + B

Reaction Rate = k[A] [B] in units of mol per liter per sec
Therefore, as the concentration of the reactants increases, so does the overall rate of the chemical reaction.
So...the rate of a chemical reaction is dependent on the concentrations of the reactants, the activation energy and the temperature of the reaction.

Chemistry 140A Winter 2014 (K. Albizati)

Acids and Bases
An early definition of acids and bases was put forth by Bronsted and Lowry:
Acid proton (hydrogen w/o an electron) donor
Base proton acceptor
Example:
H

Cl

: Cl :

:
O:

base

acid

HCl is a very strong acid, so this reaction essentially goes to completion.

Note Arrow Convention: a double headed arrow indicates movement, i.e., sharing of 2 electrons. A single-headed arrow indicates movement of
1 electron. This will apply throughout the book and throughout Chem 140A, B and C. We will use arrows to indicate electron movement.
There is a more general definition of acids and bases and one that pertains more accurately to organic species.
Lewis definition:
Acid a species which accepts electrons
Base a species which donates electrons
By this definition a base must possess an unshared electron pair and an acid must be able to accept an unshared electron pair:
Example:
O:

:
H

H+

Chemistry 140A Winter 2014 (K. Albizati)

F

CH 2CH 3

:O

CH2 CH3
F

CH 2CH 3

:O
CH2CH 3

For the purposes of organic chemistry, this is a much more generally applicable definition of acids and bases.

It is also a starting point for the discussion on electrophilicity and nucleophilicity, two important concepts in organic reactivity.
Nucleophile a species (generally electron rich) which reacts with species that are electron poor (i.e., nuclei)
Electrophile a species (generally electron poor) which reacts with species that are electron rich (has unshared electron pair(s).
Many reactions in organic chemistry can be rationalized as electrophile-nucleophile combination reactions (i.e., a plus charge seeking out a minus
charge).
A simple example:

CH3Cl

+ NaOH

CH3OH + NaCl

_
:O

OH

: Cl :
:

:
H

Cl

: :

In this reaction the hydroxide anion has electron pairs making it a nucleophilic species (a nucleophile), whereas the carbon in chloromethane has
positive charge character due to the attached highly electronegative chlorine. Hence the carbon is electrophilic (an electrophile).
This is an example of a nucleophilic substitution reaction, a very common reaction in organic chemistry. More later.
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Chemistry 140A Winter 2014 (K. Albizati)

Hence:
Nucleophiles are Lewis bases
Electrophiles are Lewis acids

More on Arrow Convention

Curved arrows show the flow of an electron pair from its origin (either a non-bonded electron pair or a covalent bond) to its destination. This is
how we depict the atomic and molecular events which occur during the course of a chemical reaction.
Some examples:

1. Dissociation of a polar covalent bond into ions

2. Formation of a covalent bond from two oppositely charged ions (the reverse of the above)

Chemistry 140A Winter 2014 (K. Albizati)

3. Simultaneous formation and dissociation of bonds

Reactions which follow this format are called substitution reactions. There are also..
4. Addition Reactions:
A. Addition of a nucleophile to a multiple bond

B. Addition of an electrophile to a multiple bond

We will encounter these four modes of reactivity many times over Chem 140A, B and C. Grasping these fundamentals of electron movement is
crucial to understanding organic reactivity.

Chemistry 140A Winter 2014 (K. Albizati)

Functional Groups
Most organic compounds consist of a carbon-atom-based backbone to which are attached one or more electronegative atoms or groups of atoms in
specific bonding arrangements, many of which are quite common. These polar atoms or arrangements of atoms are called functional groups and it is
their chemistry which is the basis of chemical reactivity of organic chemistry and therefore of life itself.
Lets look at some simple functional groups
Hydrocarbons
Hydrocarbons are compounds that contain only carbon and hydrogen atoms.
There are ALKANES which have only sp3-hybridized carbons (no multiple bonds)
Example:

H
H

C
H

H
C
H

H
C
H

C
H

H H

C C

H
C

H
C

H H H H
Octane
(n-Octane)

Propane

C
H

H
H H

C
H

H
C

C
C

H
H

H
H
H
Cyclohexane

Alkanes do not possess functional groups and hence do not have a lot of chemical reactivity. ButHydrocarbons containing one or more CC
double bonds are called ALKENES. Alkenes have appreciable reactivity and are considered a functional group.

H
C

CH3
C

H
H
Propene
(Propylene)

H
Ethene
(Ethylene)
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Chemistry 140A Winter 2014 (K. Albizati)

Hydrocarbons containing one or more CC triple bonds are called ALKYNES. These also exhibit reactivity and are functional groups.

Ethyne
(Acetylene)

CH3

Propyne

What kind of reactivity do you think is exhibited by alkenes and alkynes - nucleophilic or electrophilic?
Some other functional groups:
ALKYL HALIDES have a halogen atom:

Cl

ALCOHOLS have an O-H bond:

Chloroethane
(ethyl chloride)

ethanol
(ethyl alcohol)

ETHERS have an oxygen atom bonded to 2 carbon atoms:

Diethyl ether

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Chemistry 140A Winter 2014 (K. Albizati)

ALDEHYDES have a carbon which bears a double bond to oxygen and a hydrogen atom:

H
H

O
C
H

Acetaldehyde
(ethanal)
KETONES have a carbon doubly bonded to an oxygen and single bonds to 2 other carbons:

CARBOXYLIC ACIDS have a doubly bonded carbon (to oxygen) which also bears an O-H group:

O H

H
Acetic acid

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Chemistry 140A Winter 2014 (K. Albizati)

AMINES have a nitrogen atom with three bonds to either carbons or hydrogens:

H
H

H
N
H

Methylamine

THIOLS are the sulfur equivalent of alcohols:

Ethanethiol
Pages 68 69 have a listing of the common organic functional groups. These must be memorized. An organic compound can contain MANY
functional groups.
Throughout 140A, B and C, we will be studying the structure, reactivity and importance to society of compounds containing functional groups.
In many instances, the reactivity of functional groups has determined the course of human history.

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Chemistry 140A Winter 2014 (K. Albizati)

ALKANES
Alkanes are hydrocarbons containing no C-C multiple bonds and no atoms other than C and H. It is an important class of compounds and alkanes
make up the majority of many different kinds of fuels.
Alkanes have the general structural formula Cn H2n+2
However, just knowing the molecular formula does not tell you enough about the structure to be able to draw it unambiguously.

Isomers
Generally when we list a molecular formula of an organic compound we start with carbon, then hydrogen and then the rest of the elements in
alphabetical order.
Example:
Ethanethiol is C3H6S
Acetic acid is C2H4O2
If you were just given a formula like this, it generally would not be enough to draw out the structural formula of the molecule. You would have to
know something about the bonding arrangement because a molecule of a given molecular formula may have one of several bonding arrangements.
Example:
C5H12 can be:
H
H

n-pentane

isopentane

H
C

H
H

H
C
H

C
H

H
H

neopentane

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Chemistry 140A Winter 2014 (K. Albizati)

Compounds with the same molecular formula and different bonding patterns are called constitutional isomers. Constitutional isomers have
completely different physical properties.
Try another one:
try it without drawing out the Hs

C6H14

C
C

C
C

C
C

C
C
C

Try the isomer problems below. They make for interesting puzzles and will develop your understanding of organic molecule structure.
9 isomers of C7H16
18 isomers of C8 H18
35 isomers of C9H20
----------------------------------------------------

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Chemistry 140A Winter 2014 (K. Albizati)

Nomenclature of Organic Compounds
Nomenclature (naming) of organic compounds is crucial to being able to communicate and understand the rest of this course as well as biochem and
molecular bio courses (theres that verticality again). A long time ago, there were so few organic compounds known that they were given unique and
sometimes unusual names. This still occurs in an important branch of organic chemistry called natural products chemistry (Ex. Kimbasine). As more
and more compounds started to be discovered and OC matured, there became a need for a consistent and universally recognized naming system. The
International Union of Pure and Applied Chemistry (IUPAC) has devised a series of rules for naming organic compounds in the interest of clarity and
uniformity across international borders.

Naming Alkanes
Start out by knowing the common prefixes, based on the simple straight chain alkanes:
# Cs
1
2
3
4
5
6
7
8
9
10

Name
Methane
Ethane
Propane
Butane
Pentane
Hexane
Heptane
Octane
Nonane
Decane

Mol Formula
CH4
C2H6
C3H8
C4H10
C5H12
C6H14
C7H16
C8H18
C9H20
C10H22

Simple Structural formula

CH4
CH3CH3
CH3CH2CH3
CH3CH2CH2CH3
CH3CH2CH2CH2CH3
CH3CH2CH2CH2CH2CH3
CH3(CH2)5CH3
CH3(CH2)6CH3
CH3(CH2)7CH3
CH3(CH2)8CH3

The prefixes meth, eth, prop, but and so on are commonly used in naming compounds in science and medicine, as part of a larger name. In fact we
frequently use them to name parts or subgroups of a molecule:

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Chemistry 140A Winter 2014 (K. Albizati)

Example:
H
H

C
H

Methyl

Ethyl

Isopropyl

Propyl

These are called alkyl groups. This facilitates naming and communication quite a bit. Frequently we use a shorthand to stand for an alkyl group of
indeterminate structure. An alkyl group is abbreviated as the letter R. So we can generally abbreviate the ether functional group as

where an oxygen is attached to two alkyl groups (R groups).

We also use the letter X to stand for an indeterminate halogen atom. So the general structure of an alkyl halide is

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Chemistry 140A Winter 2014 (K. Albizati)

Types of Carbon and Hydrogen Atoms
We classify carbons according to the number of other carbons bonded to it.
A carbon with 1 carbon attached to it is a primary carbon.
A carbon with 2 carbons attached to it is a secondary carbon.
A carbon with 3 carbons attached to it is a tertiary carbon.
A carbon with 4 carbons attached to it is a quaternary carbon.
A hydrogen on a primary carbon is called a primary hydrogen and so on.
So
An imaginary hydrocarbon:
CH3
CH 3

C
C
H2

CH 3 H
2
C
C
H2

H
C

CH 3

CH3

How about:
CH 3

a component of gasoline

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Chemistry 140A Winter 2014 (K. Albizati)

How about:

HO

Cholesterol: an important molecule to all of us and a steroid

Back to naming compounds

What about more complicated compounds and compounds with functional groups?
A chemical name has 3 parts:

Prefix Parent Suffix

Prefix names and positions of substituents
Parent carbons in the longest chain
Suffix chemical family or functional group family

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Chemistry 140A Winter 2014 (K. Albizati)

IUPAC has devised a fairly simple process:
1) Find the longest carbon chain in a molecule and name it

A heptane

a nonane

This is the stem chain and forms the basis of the name.
2) Name all the groups attached to the longest carbon chain as alkyl groups

Has an ethyl and a methyl

Has a methyl and a propyl

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Chemistry 140A Winter 2014 (K. Albizati)

3) Number the longest carbon chain beginning at the end closest to a substituent
9
8

5
4

3
1

If 2 substituents are equally distant from the end of a chain, use the alphabet to decide which has priority (eg., ethyl comes before methyl) and
number accordingly.
4) Write the name of the compound according to:

Substituent groups (designated by position in the chain) - Parent name - Suffix

The substituents are placed in alphabetical order

Multiple substituents of the same identity are preceded by the prefix di, tri, tetra etc. which is preceded by the numbered
positions
9
8

5
4
6

3
2

1
3
2

4-ethyl-3-methylheptane

5
4

Cl

3-methyl-5-propylnonane

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Chemistry 140A Winter 2014 (K. Albizati)

Structural and Physical Properties of Alkanes
The 3-dimensional structures of alkanes are pretty regular. The C-C bonds tend to be about 1.54 and the C-H bonds tend to be about 1.10 and,
of course all the carbons are tetrahedral with bond angles of about 109.

109o

H
H

C
C

1.1 angstroms
H

1.54 angstroms

Most of the time we draw carbon chains in a zigzag form and this is for good reason. In the gas state the atoms try to align themselves to be as far
apart as possible
To indicate the tetrahedral nature of the bonding, we frequently draw a carbon chain with its attached hydrogens with dashed and wedged line
notation indicating this staggering of bonds.
H
H
H

C
C

H
H

Imagine the H-C-C-H in the plane of the backboard. Now imagine the wedged bonds sticking out of the plane of the board towards us and imagine
the dashed bonds going back behind the plane of the board away from us.
MODELS
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Chemistry 140A Winter 2014 (K. Albizati)

The positions of the atoms in space are not fixed, however. Molecules are quite dynamic and exhibit all kinds of molecular motions. An important
one is rotation around single bonds. In general, single bonds undergo rapid rotation at room temperature. It is logical to assume that some
arrangements of atoms will be more stable than others. Most molecules have a preferred conformation that is, a preferred arrangement of the
single bonds in space. However, many conformations are possible. A major theme in judging the stability of various conformations of a molecule
is that the atoms will try to be as far away from one another as possible so as to minimize their energy. Think of this as electron repulsion.
Consider ethane:
We can visualize and represent ethane in a number of ways.

These all show the same staggered conformation of ethane. But there are other conformations

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Chemistry 140A Winter 2014 (K. Albizati)

In the ECLIPSED conformation the hydrogens are lined up across the central C-C bond. This is the least stable conformation of ethane.

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Chemistry 140A Winter 2014 (K. Albizati)

This dynamic bond rotation can be understood with the help of an energy diagram:
HH
C
H
H

H
H

Ea = 2.9 kcal/mol

H
H

H
H
C

C
H

H
H

H
H

Torsion Angle
As the hydrogens start to become eclipsed, the energy of the system rises because electron repulsion starts to become significant. That is, the
hydrogen atoms start to become closer than their VDW radii will generally permit. The atoms want to be as far apart as possible for energy reasons.

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Chemistry 140A Winter 2014 (K. Albizati)

(Note the Elevator Phenomenon). Hence, the staggered conformation is the most stable. When two atoms are forced to be close together we say
they experience steric hindrance or steric inhibition.
Look at a bigger molecule.propane.

CH3CH2CH3
CH3
H
H

C
C

H
H

Staggered Conformation

Eclipsed Conformation

Can draw a similar energy diagram:

HCH 3
C
H
H

H
H

Ea = 3.2 kcal/mol

CH3
H

CH3
H

H
C

C
H

H
H

Torsion Angle

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Chemistry 140A Winter 2014 (K. Albizati)

In this case the energy barrier to rotation is higher because now a methyl group is eclipsed with a hydrogen.

What about n-butane?

CH3CH2CH2CH3
CH3
H
H

C
C

H
CH 3

Staggered Conformation

Eclipsed Conformation

Questions:
What is the most stable conformation?
What is the least stable conformation?
What other conformations are less stable than staggered methyls?

For practice, try drawing the energy diagram for the rotational isomers of n-butane (see page 84 of V&S).

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Chemistry 140A Winter 2014 (K. Albizati)

Reading Assignment:

All except pages 61 63 (for now)

Problem Assignment:

Skip 2.1, 2.12

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