Chapter 1
Structure and Bonding
Chapter 1 - Definitions
• Organic Chemistry – is the study of carbon containing
compounds.
• Orbitals – are the specific regions of an atom which
maintains electrons. This is defined by quantum
mechanics.
• Covalent Bond – is formed when an electron pair is
shared between atoms.
• Valance Bond Theory – maintains that bonding occurs
by the overlapping of two atomic orbitals.
Chapter 1 - Definitions
• Molecular Orbital (MO) Theory – maintains that bonds
results from the mathematical combination of atomic
orbitals to give molecular orbitals, which belong to the
entire molecule.
• Sigma (s) bonds – are bonds that are created by the
overlap of two s orbitals (sphere).
What is Organic Chemistry?
• Organic Chemistry is defined as the study of carbon
compounds.
• There are 10 atoms which are considered in organic
chemistry. These atoms are carbon, nitrogen, oxygen,
fluorine, silicon, phosphorous, sulfur, chlorine, bromine,
iodine.
Defined Organic Molecules
1
2
H
3
Li
11
Na
19
K
37
Rb
55
Cs
87
Fr
He
13
12
Al
Mg
Ca
38
Sr
56
Ba
88
Ra
C
B
Be
20
6
5
4
21
Sc
39
22
Ti
40
Y
Zr
57
72
La
89
Ac
Hf
104
Rf
23
V
41
Nb
73
Ta
105
Db
24
Cr
25
Mn
42
43
Mo
Tc
74
75
W
106
Sg
Re
107
Bh
26
Fe
44
Ru
76
Os
108
Hs
27
28
29
Co
Ni
Cu
45
46
Rh
Pd
47
77
78
Ir
109
Mt
Pt
110
Ds
Ag
79
Au
30
Zn
48
Cd
80
Hg
31
Ga
49
In
81
Tl
7
N
15
8
O
14
16
Si
P
32
33
34
Ge
50
Sn
82
Pb
As
51
Sb
83
Bi
9
S
F
17
Cl
35
10
Ne
18
Ar
Br
36
52
53
Te
I
54
84
85
86
Se
Po
At
Kr
Xe
Rn
What is Carbon so special?
• Carbon has the unique ability to bond together to form
long chains or ring structures.
• This allows carbon to make tens of billions of molecules.
• These molecules can range from DNA and plastics to
pharmaceuticals.
Review (1) - Nucleus
• An atom maintains 2 parts, the
nucleus and the shells.
• Protons, positively charge
particles, and Neutrons, neutral
charge particles are found in
the nucleus of atoms.
• Although small the nucleus
maintains all the mass of an
atom with both protons and
neutrons contributing to the
atomic mass.
• Rule: All protons and neutrons
are found in the nucleus.
Nucleus
N
N
N = Neutrons
+ = Protons
Review (2) – Electrons and Orbitals
• Electrons, negatively charge
particles, circle around and through
the nucleus in specific orbitals, which
defines the electrons path, and
shells, which defines the distance
from the nucleus. Electron are
extremely small when compared to
the nucleus and contribute nothing to
the molecular mass to the atom.
• Orbitals, are probability clouds which
determine where the electron might
be. This was determined by a
mathematical equation called a wave
equation, y.
Nucleus
1s
2s
Shells
1s Orbital
= Nucleus
= 1s Orbital
1s and 2s Orbitals
= Nucleus
= 1s Orbital
= 2s Orbital
Valance Shell
• The Valance Shell is
the outermost shell
which contains at
least one electron.
Nucleus
• In this example the 2s
is the valance shell.
1s
2s
Valence Shell = 2s
Energy Levels
2p
2s
Nucleus
1s
2s
Shells
1s
Additional Definitions
• Atomic Number (Z) – the number of protons in
the atom’s nucleus.
• Mass Number (A) – the total number of protons
and neutrons in its nucleus.
• Atomic Mass – are the weighted average mass
unit (amu) of an element’s natural occurring
isotopes is called the atomic mass (or atomic
weight).
Review (3) – Types of Orbitals
• There are many orbitals,
each with specific
number of electrons,
distance from the
nucleus, and shape.
• Specifically there are 4
different types of orbitals,
s, p, d, f with organic
chemistry focusing on the
s and p orbitals.
Nucleus
1s
2s
Shells
1s Orbital
= Nucleus
= 1s Orbital
p Orbitals
y
y
z
z
x
x
= 2py Orbital
y
y
z
z
x
x
= 2pz Orbital
= 2px Orbital
p Orbitals
y
y
z
z
x
x
= 2py Orbital
y
y
z
z
x
x
= 2pz Orbital
= 2px Orbital
Three Overlapping p Orbitals
y
z
x
= 2px Orbital
= 2py Orbital
= 2pz Orbital
2s + 2p Orbitals
y
z
x
= 2s Orbital
= 2px Orbital
= 2py Orbital
= 2pz Orbital
2s + 2p Orbitals
y
z
2p
2s
1s
x
= Nucleus
= 1s Orbital
= 2s Orbital
= 2px Orbital
= 2py Orbital
= 2pz Orbital
Review (4) - Isotopes
• Isotopes – atoms with
the same atomic number
but different mass
numbers.
Hydrogen
Nucleus
Deuterium
Nucleus
N
• This is done by the
addition of neutrons to
the nucleus of an atom.
• Remember that the mass
is from neutrons and
protons not electrons.
+ = proton
N = Neutron
Review (5) – Shell/Orbital
Differences
• Difference between a
shell and a orbital.
• An orbital is the specific
path that a pair of
electron makes around
the nucleus.
• The shell defines either
one or several orbital
that are a specific
distance away with a
node between them.
Nucleus
1s
2s
Shells
Defined Organic Molecules
1
2
H
3
Li
He
6
5
4
C
B
Be
7
N
15
11
Na
19
K
37
Rb
55
Cs
87
Fr
12
Mg
20
Ca
38
Sr
56
Ba
88
Ra
21
Sc
39
22
Ti
40
Y
Zr
57
72
La
89
Ac
Hf
104
Rf
23
V
41
Nb
73
Ta
105
Db
24
Cr
25
Mn
42
43
Mo
Tc
74
75
W
106
Sg
= Orbital (2p)
Re
107
Bh
26
Fe
44
Ru
76
Os
108
Hs
27
28
29
Co
Ni
Cu
45
46
Rh
Pd
47
77
78
Ir
109
Mt
Pt
Ag
79
Au
30
Zn
48
Cd
80
Hg
8
O
13
14
16
Al
Si
P
31
32
33
34
Ga
49
In
81
Tl
110
Ds
= Shells (1, 2, 3, 4, 5, 6)
Ge
50
Sn
82
Pb
As
51
Sb
83
Bi
9
S
Se
52
Te
84
Po
F
17
Cl
35
10
Ne
18
Ar
Br
36
53
I
54
85
86
At
Kr
Xe
Rn
Review (6) - Atomic Structure
• These numbers denote a
series of orbitals that are
a certain distance away
from the nucleus, that are
separated by a node.
• A node is a region where
electron density is zero,
or a space between
different shells.
Nucleus
1s
2s
Shells
Electronic Shells
Max, Electrons
18
Electronic Shell
N=3
3d
3p
3s
2p
8
N=2
2s
2
N=1
1s
1 S Electronic Shells
Max, Electrons
2
Electronic Shell
N=1
1s
2s + 2p Orbitals
y
z
x
= 2s Orbital
= 2px Orbital
= 2py Orbital
= 2pz Orbital
Take Home Message
•
•
•
•
General Understanding:
1) Atomic Structure
2) Valance Shell
3) Orbitals vs Shells
What are Bonds?
• Bond are the either the donation of an
electron (ionic) or the sharing of electron(s)
(covalent) between two different atoms.
Bonding
e-
e-
2 Single Hydrogen Atoms
H
H
H = 1 proton, 1 electron
1 Covalent Bond (H2)
H
ee-
H
H2 = 2 protons, 2 electrons
1 covalent bond is formed
Bonding
ee-
H
H
H
H2 = 2 protons, 2 electrons
1 covalent bond is formed
H2 = 2 protons, 2 electrons
1 covalent bond is formed
H
H
ee-
ee-
H
H2 = 2 protons, 2 electrons
1 covalent bond is formed
Energy
(too close)
HH
+
Energy
H
0
-
H H
74 pm
H
(too far)
Number of Single Bonds in Organic
Chemistry
= non-bonding electron(s)
H
O
1 Bond
2 Bonds
N
3 Bonds
C
4 Bonds
Bonds Formed
1
0
1
H
3
Li
2
3
2
4
3
2
6
7
8
5
4
C
B
Be
N
15
11
Na
19
K
37
Rb
55
Cs
87
Fr
12
Mg
20
Ca
38
Sr
56
Ba
88
Ra
21
22
Sc
Ti
39
40
Y
Zr
57
72
La
89
Ac
Hf
104
Rf
23
V
41
Nb
73
Ta
105
Db
24
Cr
25
Mn
42
43
Mo
Tc
74
75
W
106
Sg
= Orbital (2p)
Re
107
Bh
26
Fe
44
Ru
76
Os
108
Hs
27
28
29
Co
Ni
Cu
45
46
Rh
Pd
47
77
78
Ir
Pt
109
110
Mt
Ag
79
Au
30
Zn
48
Cd
80
Hg
14
16
Al
Si
P
31
32
33
34
49
In
81
Tl
Ds
= Shells (1, 2, 3, 4, 5, 6)
Ge
50
Sn
82
Pb
As
51
Sb
83
Bi
9
O
13
Ga
1
S
Se
52
Te
84
Po
F
17
Cl
35
He
10
Ne
18
Ar
Br
36
53
I
54
85
86
At
Kr
Xe
Rn
The Octet Rule
• The Octet rules states
that most organic
atoms needs 8
electrons to fill its outer
shell. Only one
example is found that
wants only 2 electrons
(HYDROGEN).
• Atoms that need 8
electrons: Carbon (C),
Nitrogen (N), Oxygen
(O), Fluorine (F),
Chlorine (Cl), Bromine
(Br), Iodine (I).
Cheat Sheet
•
•
•
•
•
(To fufill the octet) This number of bonds are formed:
4 = Carbon (C)
3 = Nitrogen (N), Phosphorus (P)
2 = Oxygen (O), Sulfur (S)
1 = Fluorine (F), Chlorine (Cl), Bromine (Br), Iodine (I),
and Hydrogen (H)
Example
• If you have 1 carbon how many chlorines do you
need?
• 1 carbon makes 4 bonds. Chlorine makes one bond.
So you need 1 carbon and 4 chlorines.
–
–
–
–
–
–
CCl4
GeCl4
AlH3
CH2Cl2
CH3NH2
CH4
Hint – (chapter 1 only)
• 1) Look for the Central Atom
• The central atoms in organic chemistry is
normally Carbon (C), Nitrogen (N), Sulfur (S),
and Oxygen (O)
• 2) Once you have the central atoms in the
molecule then they are filled in with Fluorine (F),
Chlorine (Cl), Bromine (Br), Iodine (I), and
Hydrogen (H)
Electron-Dot Structure Examples
1) Find the Central Atom.
2) Place the electrons around it. Make sure that you
fill the electrons 1 for each orbital first (4 orbitals)
until all electrons around the are used.
3) Then add the electrons from the remaining atoms.
Methane
H
H C H
H
Ethanol
H H
H C C O H
H H
Line Structures Examples
1) Find the Central Atom.
2) Place 1 straight line for each pair of electrons to
the remaining atoms.
Methane
Ethanol
H
H C H
H
H H
H C C O H
H H
Line and Electron-Dot Structures
Methane
Ethanol
H
H C H
H
H H
H C C O H
H H
H
H C H
H
H H
H C C O H
H H
sp3 Orbitals of Carbon (C)
• sp3 orbital is the combination the s and p orbitals.
• Geometry = 104.5 oC
C
109.5 o
H
C H
H
H
Bond Length
109 pm
sp3 Orbitals of Carbon (C)
• Normally you have 1s
orbital and 3p orbitals.
However in the case
of Carbon (C) the S
and P orbitals merge
to form the sp3
orbitals.
H
C H
H
H
Normal
2p
2s
1s
sp3 orbitals
2p
sp3
2s
1s
sp3 Orbitals of Carbon (C)
• sp3 orbital is the
combination the s and
p orbitals.
• Example: 4 electrons
from Carbon (C) and
4 electrons from the 4
Hydrogens (H)
sp3 orbitals
sp3
H
C H
H
H
sp2 Orbitals of Carbon (C)
Pi orbital
X
134 pm
~ 120 oC
= Flat bonds ~120 oC
Pi() bond
H
O
C
H
sp2 Orbitals of Carbon (C)
• sp2 orbitals is the
combination of 3 sp
orbitals and 1 p orbital.
1 double bond is
formed.
Normal
2p
2s
1s
sp2 orbitals
• Geometry = 120 oC flat.
H
O
C
2p
sp2
2s
H
1s
sp2 Orbitals of Carbon (C)
above
sp2 orbitals
planar
2p
sp2
below
electron
orbital
H
O
C
H
sp Orbitals of Carbon (C)
x
Z
y
o
180 C
H C C H
= Flat bonds ~180 oC
~113 pm
H C C H
sp Orbitals of Carbon (C)
• Sp orbitals is the
combination of 2 sp
orbitals and 2 p orbital.
1 triple bond is formed.
Normal
2p
2s
1s
• Geometry = 180 oC
H C C H
sp orbitals
2p
sp
2s
1s
Structure of Nitrogen, Oxygen,
Phosphorus, and Sulfur
Oxygen
Nitrogen
2 Lone Pair of Electrons
Lone Pair of Electrons
O
H N
CH3
H
CH3
H
~108.5 oC
o
~108 C
Sulfur
Phosphorus
2 Lone Pair of Electrons
O
O
P
CH3
S
O
O
~110 oC
H
CH3
~98 oC
Molecular Orbital Theory
• Combination of atomic orbitals from
different atoms to form molecular orbitals.
– All of the electrons from each atom is place
on an energy diagram which includes both a
bonding and anti-bonding level.
• Bonding is the lower level.
• Anti-bonding is the higher level.
– When the Anti-bonding level is totally filled
then the bonds are broken and the octet is
filled.
Molecular Orbital Theory
Bonding is found between two hydrogen atoms
1) Sigma anti-bonding
1) Sigma bonding
H
H
There is no bonding between two helium atoms
1) Sigma anti-bonding
1) Sigma bonding
He
He
More Complex Molecular Orbital
Diagrams
Bonding is found between two carbon atoms
2) Pi anti-bonding
2) Pi bonding
2) Sigma anti-bonding
2) Sigma bonding
1) Sigma anti-bonding
1) Sigma bonding
Carbon
(6 electrons)
Carbon
(6 electrons)
Drawing Skelton Structures
• For each carbon bond
draw a line that
represents one carbon
bound to another.
• Write out all other atoms
except hydrogens bound
to the carbon atom.
hydrogens fill in the rest of
the molecules.
• Double and triple bonds
are represented by two
and three lines
respectively.
H H
H C C O H
H H
H H
H C C O H
H H
OH
Skelton or Condensed Structures
Name
Skeleton
Total
H
H
C
H
H
C
C
C
C
H
H
H
H
Isoprene, C5H8
Phenol, C6H6O
O H
O H
H
C
H
C
C
C
C
H
C
H
H
H H H
H
C
C
C
H
H C
H
H C
C H
C
HH
H
H
H
Methylcyclohexane, C7H14
Vinyl-benzene, C8H8
H
H
H
Butane, C4H10
H
C
C
C
C
C
C
H
H
C
C
H
H
H H H
H
C
C
H
H
C
C
H
H H H
What is the Skeleton Structure?
H
O
H
N
C
H
H
C
O
H
C H
C
HC H
O
O
H
Glutamic Acid
H
H
C
C
H
C
C
H
C
C
Benzene
H
O
H
N
O
O
H H H
H C C H
C
H C C H
H H H
H
O
H
Cyclopentane
Cyclopentane
Glutamic Acid
H
H
H
H
Benzene
C
C
H
C
C
H
C
C
H
C
C
H
C
C
Naphthalene
H
H
Naphthalene
Things to Know
•
•
•
•
•
•
Orbitals
Number and Type of Bonding
Valance Shell
Octet Rule
sp3, sp2, sp orbital bonding
Electron-Dot, Line, Condensed (Skeleton)
Structures