Chapter 1

The Basics
Bonding and
Molecular
Structure
1. Introduction
Organic Chemistry is the study of
carbon compounds. Carbon, atomic
number 6, is a second-row element.
Although carbon is the principal
element in organic compounds,
most also contain hydrogen, and
many contain nitrogen, oxygen,
phosphorus, sulfur, chlorine, or
other elements
Ch.
 Most of the compounds found in
nature - those we rely on for food,
medicine, clothing (cotton, wool, silk),
and energy (natural gas, petroleum) -
are organic as well
 Chemists have learned to synthesize
millions of organic compounds never
found in nature, including synthetic
fabrics, plastics, synthetic rubber,
medicines, and even things like
photographic film & Super glue
Ch.
2. Atomic Structure
 Compounds
● made up of elements combined
in different proportions
 Elements
● made up of atoms
 Atoms
● positively charged nucleus
containing protons and neutrons
● with a surrounding cloud of
negatively charged electrons
Ch.
 Each element is distinguished by
its atomic number (Z)

 Atomic number = number of

protons in nucleus

Ch.
Ch.
2A. Isotopes

 Although all the nuclei of all

atoms of the same element will
have the same number of
protons, some atoms of the same
element may have different
masses because they have
different numbers of neutrons.
Such atoms are called isotopes

Ch.
 Examples

(1) 12
C 13
C 14
C
(6 protons (6 protons (6 protons
6 neutrons) 7 neutrons) 8 neutrons)

(2) 1
H 2
H 3
H
Hydrogen Deuterium Tritium
(1 proton (1 proton (1 proton
0 neutrons) 1 neutron) 2 neutrons)

Ch.
2B. Valence Electrons
 Electrons that surround the nucleus
exist in shells of increasing energy and
at increasing distances from the
nucleus. The most important shell,
called the valence shell, is the
outermost shell because the electrons
of this shell are the ones that an atom
uses in making chemical bonds with
other atoms to form compounds
 The number of electrons in the valence
shell (called valence electrons) is
equal to the group number of the atom
Ch.
 e.g. Carbon is in group IVA
● Carbon has 4 valence electrons

 e.g. Nitrogen is in group VA

● Nitrogen has 5 valence
electrons

 e.g. Halogens are in group VIIA

● F, Cl, Br, I all have 7 valence
electrons

Ch. 1
3. The Structural Theory of
Organic Chemistry
 Number of covalent bonds usually
formed by some elements typically
encountered in organic compounds
Eleme # of covalent Eleme # of covalent
nt bonds nt bonds
H 1 F 1
C 4 Cl 1
N 3 (or 4) Br 1
O 2 I 1
Ch. 1
 Thus
● C is tetravalent
● O is divalent
● H and halogens are monovalent

C O H Br

(tetravalent) (divalent) (monovalent)

Ch. 1
 Important:
● Do not draw any structure with
more than 4 bonds on a carbon

C C C

4 bonds

Ch. 1
 Oxygen
● Usually divalent
O

O H3C O H H3C CH3

(diethyl ether) (methanol) (acetone)

Ch. 1
 One bond on oxygen
● Usually need a negative charge
on oxygen

e.g.

O O
H OH
R O R O

Ch. 1
3A. Isomers: The Importance of
Structural Formulas
 Different compounds that have
the same molecular formula. Such
compounds are called isomers

e.g.
OH O
1-Butanol Diethyl ether

Ch. 1
● Both have the molecular formula
C4H10O

● They are constitutional isomers

● Constitutional isomers usually

have different physical
properties (e.g., melting point,
boiling point, and density) and
different chemical properties
(reactivity)
Ch. 1
3B. The Tetrahedral Shape of
Methane

Ch. 1
4. Chemical Bonds:
The Octet Rule
 Ionic (or electrovalent) bonds are
formed by the transfer of one or
more electrons from one atom to
another to create ions
 Covalent bonds result when
atoms share electrons

Ch. 1
Ch. 1 -
Electron Configuration
 Describes the position of electrons
around the atom.

Ch. 1 -
 Rules in Electron
Configuration
1. Determine the Atomic Number of
your element.
2. Follow the trend of electron
configuration.
3. Fill the electrons needed for the
configuration.
Maximum e- per subshell can
accommodate:
s=2,p=6,d=10,f=14
Ch. 1 -
Ch. 1 -
Example:

Ch. 1 -
Answer exercises:

1. C
2. Br
3. Kr
4. Mn
5. At

Ch. 1 -
Answer:

1. C- 1s2 2s2 2p2

2. Br- 1s2 2s2 2p6 3s2 3p6 4s2 3d10 4p5
3. Kr- 1s2 2s2 2p6 3s2 3p6 3d10 4s2 4p6
4. Mn- 1s2 2s2 2p6 3s2 3p6 4s2 4d5
5. At- [Xe] 4f¹⁴ 5d¹⁰ 6s² 6p⁵

Ch. 1 -
 Octet Rule
● In forming compounds, they
gain, lose, or share electrons to
give a stable electron
configuration characterized by
8 valence electrons
● When the octet rule is satisfied
for C, N, O and F, they have an
electron configuration
analogous to the noble gas Ne

Ch. 1
Ch. 1
 Recall: electron configuration of
noble (inert) gas

# of e-s in outer
shell
He [1s2] 2
Ne 1s2[2s22p6] 8
Ar 1s22s22p6[3s23p6] 8

Ch. 1
4A. Ionic Bonds

 Atoms may gain or lose electrons

and form charged particles called
ions

● An ionic bond is an attractive

force between oppositely charged
ions. Attraction force between
metals and non metals.

Ch. 1 -
 Electronegativity (EN)

● The intrinsic ability of an atom

to attract the shared electrons
in a covalent bond

● Electronegativities are based

on an arbitrary scale, with F the
most electronegative (EN =
4.0) and Cs the least (EN = 0.7)

Ch. 1 -
 element H
(EN) (2.1)
Li Be B C N O F
……..………
(1.0) (1.6) (2.0) (2.5) (3.0) (3.5) (4.0)
Na Mg Si P S Cl
………………...……
(0.9) (1.2) (1.8) (2.1) (2.5) (3.0)
K Br
………………………..…………………………………
(0.8) (2.8)
Rb I
………………………………………………..…………
(0.8) (2.5)
Cs
……………………………………………………………………
(0.7)

Ch. 1 -
 give 1 e- to
Na Cl
1s2 2s2 2p6 3s1 1s2 2s2 2p6 3s2 3p5
1 e- in outermost shell)
(7 e- in outermost shell

ionic bonding

+ –
Na Cl
1s2 2s2 2p6 1s2 2s2 2p6 3s2 3p6
8 8
Ch. 1 -
4B. Covalent Bonds & Lewis Structu
 Covalent bonds form by sharing of
electrons between atoms of similar
electronegativities to achieve the
configuration of a noble gas

 Molecules are composed of atoms

joined exclusively or predominantly
by covalent bonds

Ch. 1 -
 Example

:Cl.
: : .Cl:

: :
[Ne] 3s2 3p5 [Ne] 3s2 3p5
covalent bonding

:Cl—Cl:
: :
: :

Ch. 1 -
 Ions, themselves, may contain
covalent bonds. Consider, as an
example, the ammonium ion

H
H+ N
N H H
H H
H H
(ammonia) (ammonium cation)
(3 bonds on N) (4 bonds on N with
a positive charge on N)

Ch. 1 -
5. How to Write Lewis Structur
 Lewis structures show the
connections between atoms in a
molecule or ion using only the
valence electrons of the atoms
involved
 For main group elements, the
number of valence electrons a
neutral atom brings to a Lewis
structure is the same as its group
number in the periodic table
Ch. 1 -
 If the structure we are drawing is
a negative ion (an anion), we add
one electron for each negative
charge to the original count of
valence electrons. If the structure
is a positive ion (a cation), we
subtract one electron for each
positive charge
 In drawing Lewis structures we try
to give each atom the electron
configuration of a noble gas
Ch. 1 -
 Examples

(1) Lewis structure of CH3Br

● Total number of all valence

electrons:

C H Br

4 + 1 x 3 + 7 = 14

Ch. 1 -
● H
H C Br
H

● H

: :
H C Br:
8 H remainin
valence g6
electrons valence
electrons Ch. 1 -
(2) Lewis structure of methylamine
(CH5N)

● Total number of all valence

electrons:

C H N

4 + 1 x 5 + 5 = 14

Ch. 1 -
● H
H C N H
H H
2 valence
● electrons left
H

:
H C N H
12 H H
valence
electrons Ch. 1 -
6. Exceptions to the Octet Rule
 Elements in the 2nd row in the
periodic table usually obey the
Octet Rule (Li, Be, B, C, N, O, F)
since they have one 2s and three
2p orbitals available for bonding
 Elements in the 3rd row in the
periodic table have d orbitals that
can be used for bonding and may
not obey the Octet Rule
Ch. 1 -
Ch. 1
 Examples
Cl Cl Cl
Cl Cl Cl
Cl P P P
Cl Cl Cl Cl Cl
Cl Cl Cl
(PCl5) Phosphorus pentachloride
m.p. = 179oC
2-
F
F F
Si
F F
F

(SiF62-)
Ch. 1 -
 Some highly reactive molecules or
ions have atoms with fewer than
eight electrons in their outer shell

F
B
F F

Ch. 1 -
7. Formal Charges and How to
Calculate Them
 Formal charge number of valence
electrons -1/2 number of shared
electrons – number of unshared electrons

or F = Z - S /2 - U

where F is the formal charge, Z is the

group number of the element, S equals
the number of shared electrons, and U
is the number of unshared electrons
Ch. 1 -
 Examples
(1) The Ammonium ion (NH4+)
H
HNH Recall F = Z - S /2 - U
H
:
Formal charge of H:
= 1 – (2/2) – 0= 0
group number number
numb of of
er of H shared unshared
electron electrons Ch. 1 -
 Formal charge of N:
= 5 – (8/2)– 0= +1
group number number
numb of of
er of N shared unshared
electron H
electrons
N
s
Charge on ion = (4 x 0)+ (1x1) =
+1
 The arithmetic sum of all the
formal charges in a molecule or
ion will equal the overall charge
on the molecule or ion
Ch. 1 -
 
(2) The Nitrate ion (NO3 )

O
N Recall F = Z - S /2 - U
O O
:
To make the N atom stable, two electrons will shift from O to N (formation of a double bond
between N and O); thus N will have 8 total electrons (octet), the total number of electrons of
NO3- is 24 where 5 came from N and 18 came from three O (3x6), +1 ion is added

Formal charge of O:
= 6 – (2/2) – 6= -1
group number number
numb of of
er of O shared unshared
electron electrons Ch. 1 -
 Formal charge of O:
= 6 – (4/2) – 4 = 0
group number number
numb of of
er of O shared unshared
electron electrons
Formal scharge of N:
= 5 – (8/2)– 0= +1
group number number
numb of of
er of N shared unshared
electron electrons
Charge on sion = (2x-
O O N Ch. 1 -
(3) Water (H2O)
The sum of the formal charges
on
each atom making up a
O
molecule H H
must be zero
Formal charge of O =6–(4/2) – 4
=0
Formal charge of H = 1–(2/2) – 0
=0 O H
Charge on molecule = 0 + (2 x 0) = 0
Ch. 1 -
7A. A Summary of Formal Charges

Ch. 1 -
8. Resonance Theory
 In a Lewis structure, we draw a
well-defined location for the
electrons in a molecule. In many
molecules and ions (especially
those containing  bonds), more
than one equivalent Lewis
structure can be drawn which
represent the same molecule

Ch. 1 -
 We can write three different but
equivalent structures, 1–3

O O O
C C C
O O O O O O
1 2 3

Ch. 1 -
 O O O
becomes becomes
C C C
O O O O O O
1 2 3

 Structures 1–3, although not

identical on paper, are
equivalent; all of its carbon–
oxygen bonds are of equal length

Ch. 1 -
 Resonance theory states that whenever
a molecule or ion can be represented by
two or more Lewis structures that differ
only in the positions of the electrons, two
things will be true:
● None of these structures, which we call
resonance structures or resonance
contributors, will be a realistic
representation for the molecule or ion.
None will be in complete accord with the
physical or chemical properties of the
substance
● The actual molecule or ion will be better
represented by a hybrid (average) of these
structures
Ch. 1 -
 ● Resonance structures, then,
are not real structures for the
actual molecule or ion; they
exist only on paper

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

Ch. 1 -
● It is also important to distinguish
between resonance and an
equilibrium

● In an equilibrium between two or

more species, it is quite correct to
think of different structures and
moving (or fluctuating) atoms, but not
in the case of resonance (as in the
carbonate ion). Here the atoms do not
move, and the “structures” exist only
on paper. An equilibrium is indicated
by and resonance by
Ch. 1 -
 Examples
(1) Benzene

(2) Carboxylate ion (RCOO-)

O O O

R O R O R O

(3) Ozone (O3)

O O
O O O O Ch. 1 -
10. Atomic Orbitals and Electron
Configuration

Ch. 1 -
10A. Electron Configurations
 The relative energies of atomic orbitals in
the 1st & 2nd principal shells are as follows:
● Electrons in 1s orbitals have the lowest
energy because they are closest to the
positive nucleus
● Electrons in 2s orbitals are next lowest in
energy
● Electrons of the three 2p orbitals have
equal but higher energy than the 2s
orbital
● Orbitals of equal energy (such as the
three 2p orbitals) are called degenerate
orbitals
Ch. 1 -
 Aufbau principle
● Orbitals are filled so that those
of lowest energy are filled first

 Pauli exclusion principle

● A maximum of two electrons
may be placed in each orbital
but only when the spins of the
electrons are paired

Ch. 1 -
 Hund’s rule
● When we come to orbitals of equal
energy (degenerate orbitals) such
as the three p orbitals, we add one
electron to each with their spins
unpaired until each of the
degenerate orbitals contains one
electron. (This allows the
electrons, which repel each other,
to be farther apart.) Then we
begin adding a second electron to
each degenerate orbital so that the
spins are paired Ch. 1 -
Ch. 1 -
12. The Structure of Methane an
Ethane: sp3 Hybridization

Ground state of a carbon atom

C
1s 2s 2px 2py 2pz

Ch. 1 -
 Hybridization
● sp3
sp3
covalent hybridized
bond H carbon
H C H
H
(line bond structure)

Ch. 1 -
 Hybridization
● sp3 H
H C H
H
(Lewis structure)

109o H Tetrahedral
structure
C H
H H
Carbon with
(3-D stucture) 4 bonds
Ch. 1 -
12A. The Structure of Methane

Ch. 1 -
Ch. 1 -
Ch. 1 -
Ch. 1 -
12B. The Structure of Ethane

Ch. 1 -
Ch. 1 -
13. The Structure of Ethene
(Ethylene): sp2 Hybridization
 sp2
1  bond + 1  bond
o
~120
H H
~120o C C sp2 hybridized carbon
H H
o
~120

Ch. 1 -
Ch. 1 -
Ch. 1 -
13A. Restricted Rotation and the
Double Bond
 There is a large energy barrier to
rotation associated with groups
joined by a double bond
● ~264 kJmol-1 (strength of the 
bond)
● To compare: rotation of groups
joined by C-C single bonds
~13-26 kJmol-1
Ch. 1 -
14. The Structure of Ethyne
(Acetylene): sp Hybridizatio
 sp
1  bond + 2  bond
H C C H
180o 2
sp hybridized carbon

Linear structure
Carbon with (2 + 2 ) bonds

Ch. 1 -
Ch. 1 -
Ch. 1 -
Ch. 1 -
 sp orbital
● 50% s character, 50% p
character

 sp2 orbital
● 33% s character, 66% p
character

 sp3 orbital
● 25% s character, 75% p
character
Ch. 1 -
Ch. 1 -
Ch. 1 -
17. How to Interpret and Write
Structural Formulas

Ch. 1 -
17A. Dash Structural Formulas
 Atoms joined by single bonds can
rotate relatively freely with
respect to one another
H
H HH H H H H
H HO H
C C H H C O
C C
H C O C C
H C H
H H H HH H
H H
Equivalent dash formulas for propyl alcohol

Ch. 1 -
17B. Condensed Structural Formul

Ch. 1 -
17C. Bond-Line Formulas

Ch. 1 -
Ch. 1 -
17D. Three-Dimensional Formulas
H
H H H
C H H
OR C C etc.
H C H
H H H
H
Ethane

H H Br
C OR C OR C etc.
H H H
Br Br H
H H H
Bromomethane
Ch. 1 -
 Br
H

H OH Cl
H
Examples of bond-line formulas that include
three-dimensional representations

H NH
2 Br H
HO

An example involving An example involving

trigonal planar geometry linear geometry
Ch. 1 -
 END OF CHAPTER 1 

Ch. 1 -