Organic

Chemistry
1-1

Review of
Molecular
Structure
Chapter 1
1-2

Organic Chemistry

The study of the compounds of carbon

Over 10 million compounds have been identified
about 1000 new ones are identified each day!

C is a small atom

it forms single, double, and triple bonds

it is intermediate in electronegativity (2.5)
it forms strong bonds with C, H, O, N, and some metals

1-3

Schematic View of an Atom

a small dense nucleus,
diameter 10-14 - 10-15 m,
which contains positively
charged protons and
most of the mass of the
atom
an extranuclear space,
diameter 10-10 m, which
contains negatively
charged electrons

1-4

Electron Configuration of Atoms

Electrons are confined to regions of space called

principle energy levels (shells)
each shell can hold 2n2 electrons (n = 1,2,3,4......)
Number of
Relative Energies
Electrons Shell
of Electrons
Shell
Can Hold
in These Shells
higher
4
32
3
18
2
8
1
2
lower

1-5

Electron Configuration of Atoms

Shells are divided into subshells called orbitals,

which are designated by the letters s, p, d, f,........
s (one per shell)
p (set of three per shell 2 and higher)
d (set of five per shell 3 and higher) .....

Shell Orbitals Contained in That Shell

3

3s, 3px , 3p y, 3pz, plus five 3d orbitals

2
1

2s, 2px , 2p y, 2pz

1s

1-6

Electron Configuration of Atoms

Aufbau Principle:

orbitals fill in order of increasing energy from lowest

energy to highest energy

Pauli Exclusion Principle:

only two electrons can occupy an orbital and their

spins must be paired

Hunds Rule:

when orbitals of equal energy are available but there

are not enough electrons to fill all of them, one
electron is added to each orbital before a second
electron is added to any one of them
1-7

Electron Configuration of Atoms

The pairing of electron spins

1-8

Electron Configuration of Atoms

Table 1.3 The Ground-State Electron

Configuration of Elements 1-18

1-9

Lewis Dot Structures

Gilbert N. Lewis
Valence shell:

the outermost occupied electron shell of an atom

Valence electrons:

electrons in the valence shell of an atom; these

electrons are used to form chemical bonds and in
chemical reactions

Lewis dot structure:

the symbol of an element represents the nucleus and

all inner shell electrons
dots represent valence electrons
1-10

Lewis Dot Structures

Lewis Dot Structures for Elements 1-18
1A

2A

H.

Al :

.
.
C: N :
.

Si : . P:

: O:
.
.
:S :
.

:F :
.

: Cl :

8A
He :
: Ne :

: :

7A

Na. Mg:

B:

5A 6A

: :

Be :

4A

Li .

3A

: Ar :

1-11

Lewis Model of Bonding

Atoms bond together so that each atom acquires

an electron configuration the same as that of the
noble gas nearest it in atomic number
an atom that gains electrons becomes an anion
an atom that loses electrons becomes a cation
the attraction of anions and cations leads to the
formation of ionic solids
an atom may share electrons with one or more atoms
to complete its valence shell; a chemical bond formed
by sharing electrons is called a covalent bond
bonds may be partially ionic or partially covalent;
these bonds are called polar covalent bonds
1-12

Covalent Bonds

The simplest covalent bond is that in H2

the single electrons from each atom combine to form
an electron pair
H

H-H

H0 = -435 kJ (-104 kcal)/mol

the shared pair functions in two ways simultaneously;

it is shared by the two atoms and fills the valence shell
of each atom

The number of shared pairs

one shared pair forms a single bond

two shared pairs form a double bond
three shared pairs form a triple bond
1-13

Lewis Structures

To write a Lewis structure

determine the number of valence electrons

Atombyatomanalysis
determine the arrangement of atoms
Differentarrangementsarealmostalwayspossibleisomers
connect the atoms by single bonds
arrange the remaining electrons so that each atom has
a complete valence shell
Usecommonbondingpatternsasyourguide
show a bonding pair of electrons as a single line
show a nonbonding pair of electrons as a pair of dots
1-14

Stable Bonding in Neutral Molecules

In neutral molecules

hydrogen has one bond

carbon has 4 bonds and no lone pairs
nitrogen has 3 bonds and 1 lone pair
oxygen has 2 bonds and 2 lone pairs
halogens have 1 bond and 3 lone pairs
3rd row and transition metal bonding patterns are more
complicated but we dont encounter a lot of them here

1-15

Multiple Bonding
Bonded atoms can share more than one pair of
electrons to form multiple bonds
Molecular oxygen (O2) has a double bond
between the oxygen atoms
+

gives

1-16

Lewis Structures H-O-H

H2 O (8)
Water
H
H
C C
H
H
C2 H4 (12)
Ethylene

H-N-H
H
NH3 (8)
Ammonia
H-C C-H
C2H2 (10)
Acetylene

H
H-C-H
H
CH4 (8)
Methane
H
C O
H
CH2O (12)
Formaldehyde

H-Cl
HCl (8)
Hydrogen chloride
O
H

H2CO3 (24)
Carbonic acid

1-17

Electronegativity
Electronegativity:

a very crude measure of an atoms attraction for the

electrons it shares with another atom in a chemical
bond

Pauling scale

generally increases left to right in a row

generally increases bottom to top in a column

1-18

Polar and Nonpolar Covalent Bonds

Although all covalent bonds involve sharing of

electrons, they differ widely in the degree of
sharing
We divide covalent bonds into
nonpolar covalent bonds
polar covalent bonds

Difference in
Electronegativity
Between Bonded Atoms
Less than 0.5
0.5 to 1.9
Greater than 1.9

Type of Bond
Nonpolar covalent
Polar covalent
Ions form
1-19

Polar and Nonpolar Covalent Bonds

an example of a polar covalent bond is that of H-Cl
the difference in electronegativity between Cl and H is
3.0 - 2.1 = 0.9
we show polarity by using the symbols + and -, or by
using an arrow with the arrowhead pointing toward the
negative end and a plus sign on the tail of the arrow at
the positive end
+ H Cl

Cl

1-20

Polar Covalent Bonds

Bond dipole moment ():

a measure of the polarity of a covalent bond

the product of the charge on either atom of a polar
bond times the distance between the nuclei
average bond dipole moments of selected covalent
bonds
Bond
Dipole
Bond (D)

H-C
H-N
H-O
H-S

0.3
1.3
1.5
0.7

Bond
Dipole
Bond (D)

C-F
C-Cl
C-Br
C-I

1.4
1.5
1.4
1.2

Bond
Dipole
Bond (D)

C-O
C=O
C-N
-C=N

0.7
2.3
0.2
3.5
1-21

Polar and Nonpolar Molecules

To determine if a molecule is polar, we need to

determine
if the molecule has polar bonds
the arrangement of these bonds in space

Molecular dipole moment (): the vector sum of

the individual bond dipole moments in a
molecule
reported in debyes (D)

1-22

Polar and Nonpolar Molecules

these molecules have polar bonds, but each has

a zero dipole moment

Cl

F
O

F
Carbon dioxide
=0D

Boron trifluoride
=0D

C
Cl
Cl

Cl

Carbon tetrachloride
=0D

1-23

Polar and Nonpolar Molecules

these molecules have polar bonds and are polar

molecules
direction
of dipole
moment

Water
= 1.85D

H
Ammonia
= 1.47D

direction
of dipole
moment

1-24

Polar and Nonpolar Molecules

formaldehyde has polar bonds and is a polar molecule
direction
of dipole
moment

O
C

Formaldehyde
= 2.33 D

1-25

Formation of Ions

A rough guideline:

ions will form if the difference in electronegativity

between interacting atoms is 1.9 or greater
example: sodium (EN 0.9) and fluorine (EN 4.0)
we use a single-headed (barbed) curved arrow to show
the transfer of one electron from Na to F
F

Na

Na

in forming Na+F-, the single 3s electron from Na is

transferred to the partially filled valence shell of F
Na(1s22s 22p63s1 ) + F(1s 22s2 2p5 )

Na+(1s2 2s22p6) + F-(1s2 2s2 2p6 )

1-26

Formal Charge

Formal charge: the charge on an atom in a

molecule or a polyatomic ion
To derive formal charge

1. write a correct Lewis structure for the molecule or ion

2. assign each atom all its unshared (nonbonding)
electrons and one-half its shared (bonding) electrons
3. compare this number with the number of valence
electrons in the neutral, unbonded atom
Formal
charge

Number of
= valence electrons
in the neutral,
unbonded atom

All
One half of
unshared + all shared
electrons
electrons
1-27

Formal Charge

Example: Draw Lewis structures, and show which atom in

each bears the formal charge

(a) NH2

(b) HCO3

(c) CO3

+
(d) CH3 NH3

(e) HCOO

(f) CH3COO

2-

1-28

Exceptions to the Octet Rule

Molecules containing atoms of Group 3A

elements, particularly boron and aluminum

Boron trifluoride

:Cl

Al
:Cl :

:F :

:Cl :

: :

: :

:F

6 electrons in the
valence shells of boron
and aluminum

: F:

Aluminum chloride

1-29

Exceptions to the Octet Rule

Atoms of third-period elements have 3d orbitals

and may expand their valence shells to contain
more than 8 electrons
Sulfur, phosphorus may have up to 10

1-30

Resonance

For many molecules and ions, no single Lewis

structure provides a truly accurate
representation
O

O
and

H3 C C
O

H3 C C
O

Ethanoate ion
(acetate ion)

1-31

Resonance

Linus Pauling - 1930s

many molecules and ions are best described by

writing two or more Lewis structures
individual Lewis structures are called contributing
structures
connect individual contributing structures by doubleheaded (resonance) arrows
the molecule or ion is a hybrid of the various
contributing structures

1-32

Resonance

Examples: equivalent contributing structures

CH3

O:

C
:O:-

Nitrite ion
(equivalent contributing
structures)

O:

CH3

:O :-

:N
O:

: O:-

O:

:N

:O:-

Acetate ion
(equivalent contributing
structures)

1-33

Resonance

Curved arrow: a symbol used to show the

redistribution of valence electrons
In using curved arrows, there are only two
allowed types of electron redistribution:
from a bond to an adjacent atom
from an atom to an adjacent bond

Electron pushing is a survival skill in organic

chemistry
learn it well!

1-34

Resonance

All contributing structures must

1. have the same number of valence electrons

2. obey the rules of covalent bonding
no more than 2 electrons in the valence shell of H
no more than 8 electrons in the valence shell of a 2nd
period element
3rd period elements, such as P and S, may have up to
12 electrons in their valence shells
3. differ only in distribution of valence electrons; the
position of all nuclei must be the same
4. have the same number of paired and unpaired electrons
1-35

Resonance

The carbonate ion, for example

a hybrid of three equivalent contributing structures

the negative charge is distributed equally among the
three oxygens

1-36

Resonance

Preference 1: filled valence shells

structures in which all atoms have filled valence shells

contribute more than those with one or more unfilled
valence shells
+
CH3 O

H
Greater contribution;
both carbon and oxygen have
complete valence shells

CH3 O

+
C

H
Lesser contribution;
carbon has only 6 electrons
in its valence shell

1-37

Resonance

Preference 2: maximum number of covalent

bonds

structures with a greater number of covalent bonds

contribute more than those with fewer covalent bonds
CH3

+
O

H
Greater contribution
(8 covalent bonds)

CH3 O

+
C

H
Lesser contribution
(7 covalent bonds)

1-38

Resonance

Preference 3: least separation of unlike charge

structures with separation of unlike charges contribute

less than those with no charge separation

Greater contribution
(no separation of
unlike charges)

:O: -

O:
CH3 -C-CH3

CH3 -C-CH3
Lesser contribution
(separation of unlike
charges)

1-39

Resonance

Preference 4: negative charge on the more

electronegative atom

structures that carry a negative charge on the more

electronegative atom contribute more than those with
the negative charge on the less electronegative atom
O
(1)

C
H3 C

O
CH3

(a)
Lesser
contribution

(2)

C
H3 C

CH3

(b)
Greater
contribution

C
H3 C

CH3

(c)
Should not
be drawn

1-40

Structural Formulas

Lewis structures indicate atom connectivity

Do not show 3-D structure, but it is there

Drawing Lewis structures of large molecules can

get cumbersome
Use shortcuts to simplify things
Rely on normal bonding properties of atoms

Types include

Condensed structural formulas

Line-angle formulas

All subsets of molecular formula

1-41

Condensed Structural formulas

Based on typical bonding patterns

Carbon makes 4 bonds in stable molecules

Oxygen makes 2 bonds and has 2 lone pairs
Nitrogen makes 3 bonds and has 1 lone pair

Show molecule by groups centered on carbon

CH4
CH3CH2CH3
CH3CH3

or
(CH3)2CH2

CH3CH(CH3)CH3
(CH3)3CH

1-42

Which is the correct Lewis structure?

(CH3)2CH(CH2)2CH(CH3)2

1-43

Can add heteroatoms (N, O, halogens) and multiple bonds

CH3CH2OH

CH3CH2NHCH3

CH3CHClCH3

CH3CH=CHCH3

1-44

Line-Angle structures

Lines to represent bonds

skeletal structures

Carbons are not drawn, but occur at

Intersections
Vertices (ends of lines)

Hydrogens are not usually shown

assumed to be as many as needed to fulfill carbon

valency
CH3(CH2)4CH3

1-45

Heteroatoms are shown explicitly WITH Hydrogens

*
*

How many hydrogens are present at marked position?

A. 0 B. 1 C. 2 D. 3 E. 4
1-46

Combined structures are allowed BUT

if you show C atoms, you MUST show the 4 bonds to it
(including H)
NOT OK

(C14H30)
OK`

Trivalent carbon

1-47

Find the acceptable structure

A

E
1-48

Trivalent carbon can be possible for ions and radicals

one missing electron around carbon
(3 net electrons)

One for each bond (3) no more

(electron deficient)

one extra electron around carbon

(5 net electrons)

_
3 from the bonds, must have a nonbonded lone pair (note that it has an
octet even!)

Pentavalent carbon (5 bonds to C) is NEVER

acceptable in this class

1-49

Acids
and
Bases
1-50

Arrhenius Acids and Bases

In 1884, Svante Arrhenius proposed these

definitions

acid: a substance that produces H3O+ ions aqueous

solution
base: a substance that produces OH- ions in aqueous
solution
this definition of an acid is a slight modification of the
original Arrhenius definition, which was that an acid
produces H+ in aqueous solution
today we know that H+ reacts immediately with a water
molecule to give a hydronium ion
H+(aq) + H2O(l)

H3 O+(aq)
Hydronium ion
1-51

Brnsted-Lowry Definitions

Acid: a proton donor

Base: a proton acceptor
H O:

: :

+
H O H + :O

+ H O

H
Proton
donor

Proton
acceptor

H
Proton
donor

H O:

H
Proton
acceptor

H
+
H O H + :N

H
+
+ H N H
H

1-52

Conjugate Acids & Bases

conjugate base: the species formed from an acid when
it donates a proton to a base
conjugate acid: the species formed from a base when
it accepts a proton from an acid
acid-base reaction: a proton-transfer reaction
conjugate acid-base pair: any pair of molecules or ions
that can be interconverted by transfer of a proton
conjugate acid-base pair
conjugate acid-base pair
HCl(aq)
Hydrogen
chloride
(acid)

H2O(l)
Water
(base)

Cl-(aq)
+ H3 O (aq)
Chloride
Hydronium
ion
ion
(conjugate
(conjugate
base of HCl) acid of H2O)

1-53

Conjugate Acids & Bases

Brnsted-Lowry definitions do not require water as a
reactant
consider the following reaction between acetic acid
and ammonia
conjugate acid-base pair

conjugate acid-base pair

CH3 COOH + NH3
Acetic acid Ammonia
(acid)

(base)

CH3 COO- +
NH4 +
Acetate
Ammonium
ion
ion
(conjugate base (conjugate acid
acetic acid)
of ammonia)

1-54

Conjugate Acids & Bases

we can use curved arrows to show the flow of
electrons in an acid-base reaction
: :

H
+
:N H
H
Acetic acid
Ammonia
(proton donor) (proton acceptor)

: O:
H
CH3 -C-O: + H-N-H
H
Acetate ion Ammonium
ion

: :

: O:
CH3 -C-O H

1-55

Conjugate Acids & Bases

Many organic molecules have two or more sites

that can act as proton acceptors

in these molecules, the favored site of protonation is

the one in which the charge is more delocalized
question: which oxygen of a acetic acid is protonated?

O
CH3 -C-O-H + H2 SO4
acetic acid

+ H
O

+
CH3 -C-O-H or
CH3 -C-O-H + HSO4
H
A
B
(protonation
(protonation
on the
on the
carbonyl oxygen) hydroxyl oxygen)
1-56

Conjugate Acids & Bases

for protonation on the carbonyl oxygen, we can write

three contributing structures
two place the positive charge on oxygen, one places it
on carbon
+ H
O
CH3 -C-O-H

H
O
+
CH3-C-O-H
-C

A-1
(C and O have
complete octets)

A-2
(C has incomplete
octet)

H
O
+
CH3 -C=O-H
A-3
(C and O have
complete octets)

A-1 and A-3 make the greater contribution because all

atoms have complete octets
the positive charge is delocalized over three atoms
1-57
with the greater share on the two equivalent oxygens

Conjugate Acids & Bases

for protonation on the hydroxyl oxygen, we can write

two contributing structures
O

+
CH3 -C-O-H
H
B-1

+
CH3 -C-O-H
+
H
B-2
(charge separation and
adjacent positive charges)

B-2 makes only a minor contribution because of

charge separation and adjacent positive charges
therefore, we conclude that protonation of a carboxylic
acid occurs preferentially on the carbonyl oxygen
1-58

Conjugate Acids & Bases

Does proton transfer to acetamide occur

preferentially on the oxygen or the nitrogen?
O
CH3 -C-N-H + HCl
H
Acetamide
(an amide)

+ H
O
CH3 -C-N-H or
H
A
(protonation
on the
amide oxygen)

OH
+
CH3-C-N-H + Cl
H
B
(protonation
on the
amide nitrogen)

1-59

Acids & Base Strengths

The strength of an acid is expressed by an

equilibrium constant

the acid dissociation of acetic acid is given by the

following equation
O
CH3COH + H2 O
Acetic acid Water

CH3CO
Acetate
ion

+ H3O
Hydronium
ion

1-60

Weak Acids and Bases

We can write an equilibrium expression for the

dissociation of any uncharged acid, HA, as:
+
A + H3 O

HA + H2 O
Keq =

[H3 O ][A ]
[HA][H2 O]

water is a solvent and its concentration is a constant

equal to approximately 55.5 mol/L
we can combine these constants to give a new
constant, Ka, called an acid dissociation constant
K a = Keq[H2 O] =

[H3 O+][A-]
[HA]
1-61

Acid
Weaker Ethane
acid
Ethylene
Ammonia
Hydrogen
Acetylene
Ethanol
Water

CH2 =CH2
NH3
H2
HC CH
CH3CH2OH
H2 O

Methylammonium ion CH3NH3

Bicarbonate ion
Phenol
Ammonium ion
Hydrogen sulfide
Carbonic acid
Acetic acid
Benzoic acid
Phosphoric acid
Hydronium ion
Sulfuric acid
Hydrogen chloride
Stronger Hydrogen bromide
acid
Hydrogen iodide

pKa

Formula
CH3CH3

HCO3
C6H5 OH
+
NH4
H2 S
H2 CO3
CH3COOH
C6H5 COOH
H3 PO4
+
H3 O
H2 SO4
HCl
HBr
HI

51
44
38
35
25
15.9
15.7

10.64
10.33
9.95
9.24
7.04
6.36
4.76
4.19
2.1
-1.74
-5.2
-7
-8
-9

Conjugate Base
CH3CH2
Stronger
- conjugate
CH2 =CH
base
NH2
H
HC C
CH3CH2O
HO
CH3NH2
2-

CO3
C6H5 O
NH3
HS
HCO3
CH3COO
C6H5 COO
H2 PO4
H2 O
HSO4
Cl
Weaker
Br
conjugate
base
I

1-62

Acid-Base Equilibria

Equilibrium favors reaction of the stronger acid

and stronger base to give the weaker acid and
weaker base
CH3COOH

NH3

Acetic acid
Ammonia
(stronger base)
pKa 4.76
(stronger acid)

CH3 COO

NH4 +

Acetate ion Ammonium ion

(weaker base)
pKa 9.24
(weaker acid)

pKeq = 4.76 - 9.24 = -4.48

Ke q = 3.0 x 104

1-63

Acid-Base Equilibria

Consider the reaction between acetic acid and

sodium bicarbonate

we can write the equilibrium as a net ionic equation

we omit Na+ because it does not undergo any
chemical change in the reaction
O

HCO3CH3COH +
Acetic acid
Bicarbonate ion
pKa 4.76
(stronger acid)

CH3CO +
H2 CO3
Acetate ion Carbonic acid
pKa 6.36
(weaker acid)

equilibrium lies to the right

carbonic acid forms, which then decomposes to
carbon dioxide and water

1-64

Lewis Acids and Bases

Lewis acid: any molecule of ion that can form a

new covalent bond by accepting a pair of
electrons
Lewis base: any molecule of ion that can form a
new covalent bond by donating a pair of
electrons
A
Lewis
acid

:B
Lewis
base

+
A B

new covalent bond

formed in this Lewis
acid-base reaction

1-65

Lewis Acids and Bases

examples
:

H :Br :

H H
sec-Butyl cation
(a carbocation)
CH3 CH 2

: :

+
CH3 -C C-CH3

:Br : Bromide
ion

F
B F

CH3 -C

C-CH3

H H
2-Bromobutane

CH3 CH 2

F
+
:O:
+
:O B-F
CH3 CH 2
F
F
CH3 CH 2
Diethyl ether Boron trifluoride A BF3-ether complex
(a Lewis base) (a Lewis acid)

1-66

Lewis Acids include Bronsted Acids

A proton (H+) is a Lewis acid
Proton donors therefore accept a pair of electrons to form a
new covalent bond between the base and proton

A covalent bond is also broken but that doesnt

matter
The definition of Lewis acid doesnt say anything about not
breaking bonds
All that matters is that it can ACCEPT a pair of electrons

Hydroxide (OH) is clearly a Lewis base

Other things are bases in Lewis approach (ammonia, halide
ions)

Most neutral molecules are acids and bases

However,
in acid/base+strength
NH2 they
+ H3can
O+ be
very
:NHdifferent
+
H
+ OH
3
2O NH4
pKa(NH3) = 38

pKa(NH4+) = 9

1-67