Chemisty structure of atoms.....

Structure and Bonding
The Periodic Table

 The nucleus contains positively charged protons and
uncharged neutrons.
 The electron cloud is composed of negatively charged
electrons.
1

The Periodic Table
Figure 1.1
A comparison of two isotopes
of the element carbon

• Elements in the same row are similar in size.
• Elements in the same column have similar electronic
and chemical properties.
2

Figure 1.2
A periodic table of the
common elements seen
in organic chemistry

3

• An s orbital has a sphere of electron density and is lower
in energy than the other orbitals of the same shell.
• A p orbital has a dumbbell shape and contains a node of
electron density at the nucleus. It is higher in energy than
an s orbital.

4

Since there is only one orbital in the first shell, and each shell can
hold a maximum of two electrons, there are two elements in the first
row, H and He.

Each element in the second row of the periodic table has four orbitals
available to accept additional electrons: one 2s orbital, and three 2p
orbitals.

5

Second Row Elements
• Since each of the four orbitals available in the second
shell can hold two electrons, there is a maximum
capacity of eight electrons for elements in the second
row.
• The second row of the periodic chart consists of eight
elements, obtained by adding electrons to the 2s and
three 2p orbitals.

6

1.1) Oxygen has 3 isotopes: 16O, 17O, and 18O. Give
the number of protons, neutrons and electrons in
each species.
16O

17O

18O

protons

8

8

8

neutrons

8

9

10

electrons

8

8

8

7

Atomic Number = Number of protons
Number of Neutrons = Mass Number – Atomic Number
Number of protons = Number of electrons
For 147N, give the number of total electrons and the
number of valence electrons
Atomic number is 7 which means 7 protons which means
7 electrons.

Nitrogen is a second row element so subtract 2
electrons for the 1s shell leaving 5 valence electrons.

8

Review of Bonding
• Bonding is the joining of two atoms in a stable
arrangement.

• Through bonding, atoms attain a complete outer shell
of valence electrons.
• Through bonding, atoms attain a stable noble gas
configuration.
• Ionic bonds result from the transfer of electrons from
one element to another.
• Covalent bonds result from the sharing of electrons
between two nuclei.
9

• An ionic bond generally occurs when elements on the
far left side of the periodic table combine with elements
on the far right side, ignoring noble gases.
• A positively charged cation formed from the element on
the left side attracts a negatively charged anion formed
from the element on the right side. An example is
sodium chloride, NaCl.

10

Bonding in Molecular Hydrogen (H2)
• Hydrogen forms one covalent bond.
• When two hydrogen atoms are joined in a bond, each
has a filled valence shell of two electrons.

11

• Second row elements can have no more than eight
electrons around them. For neutral molecules, this has
two consequences:
 Atoms with one, two, or three valence electrons form one,
two, or three bonds, respectively, in neutral molecules.
 Atoms with four or more valence electrons form enough
bonds to give an octet. This results in the following
equation:

 When second-row elements form fewer than four bonds
their octets consist of both bonding (shared) and
nonbonding (unshared) electrons. Unshared electrons are
also called lone pairs.
12

Figure 1.3
Summary: The usual number
of bonds of common
neutral atoms

13

Label the following as either ionic or covalent bonded
molecules.
F2

CH3CH3 Covalent (C-C and
C-H)

covalent

LiBr ionic

NaNH2 Ionic (Na-N)

Covalent (N-H)
How many covalent bonds are predicted for each
atom

O 2

Al

3

Br 1

For atoms having more than 3 valence electrons
Total electrons – valence electrons = bonds

14

Review of Lewis Structures
Lewis structures are electron dot representations for
molecules. There are three general rules for drawing
Lewis structures:
1. Draw only the valence electrons.
2. Give every second-row element an octet of electrons,
if possible.
3. Give each hydrogen two electrons.

In a Lewis structure, a solid
line indicates a two-electron
covalent bond.

15

Formal Charge
• Formal charge is the charge assigned to individual atoms in a
Lewis structure.
• By calculating formal charge, we determine how the number
of electrons around a particular atom compares to its number
of valence electrons. Formal charge is calculated as follows:

• The number of electrons ―owned‖ by an atom is determined
by its number of bonds and lone pairs.

• An atom ―owns‖ all of its unshared electrons and half of its
shared electrons.
16

The number of electrons ―owned‖ by different atoms is
indicated in the following examples:
Example 1
Example 3

Example 2

17

Draw the Lewis structure for CH5N.
Arrange H’s around periphery.

H
H C N H
H H

Count valence electrons

1C x 4 e-s = 4
5H x 1 e- = 5
1N x 5 e-s = 5

total e-s = 14
Assign 2 e-s to each bond to hydrogen and fill the
octets of the other atoms
H
H

C

H

H
N

H
19

Draw the Lewis structure for HCN
Arrange H’s around periphery.

Count valence electrons

H C N

1C x 4 e-s = 4
1H x 1 e- = 1
1N x 5 e-s = 5

total e-s = 10
Assign 2 e-s to each bond to hydrogen and fill the
octets of the other atoms
H

4

C

e-s

N

used

6 e-s left
H

C

N
20

Assign formal charge for each atom in the
following molecule.
4 – (0 + (1/2 X 6))= +1
O

6 – (4 + (1/2 X 4))= 0

C

O

6 – (6 + (1/2 X 2))= -1

Overall formal charge of molecule is 0.

21

Isomers
In drawing a Lewis structure for a molecule with several
atoms, sometimes more than one arrangement of atoms is
possible for a given molecular formula.
Example:

Both are valid Lewis structures and both molecules exist.
These two compounds are called isomers.
Isomers are different molecules having the same
molecular formula. Ethanol and dimethyl ether are
constitutional isomers.
22

Exceptions to the Octet Rule
Elements in Groups 2A and 3A

Elements in the Third Row

23

Resonance
Some molecules cannot be adequately represented by a single
Lewis structure. For example, two valid Lewis structures can be
drawn for the anion (HCONH)¯. One structure has a negatively
charged N atom and a C-O double bond; the other has a
negatively charged O atom and a C-N double bond.

These structures are called resonance structures or resonance
forms. A double headed arrow is used to separate the two
resonance structures.
24

Introduction to Resonance Theory
Regarding the two resonance forms of (HCONH)¯ shown
below, it should be noted that:

• Neither resonance structure is an accurate representation
for (HCONH)¯. The true structure is a composite of both
resonance forms and is called a resonance hybrid.
• The hybrid shows characteristics of both structures.
• Resonance allows certain electron pairs to be delocalized
over two or more atoms, and this delocalization adds
stability.
• A molecule with two or more resonance forms is said to be
25
resonance stabilized.

The following basic principles of resonance theory should
be kept in mind:
1. Resonance structures are not real. An individual
resonance structure does not accurately represent the
structure of a molecule or ion. Only the hybrid does.
2. Resonance structures are not in equilibrium with each
other. There is no movement of electrons from one form
to another.
3. Resonance structures are not isomers. Two isomers
differ in the arrangement of both atoms and electrons,
whereas resonance structures differ only in the
arrangement of electrons.
26

Drawing Resonance Structures
Rule [1]: Two resonance structures differ in the position of multiple
bonds and nonbonded electrons. The placement of atoms and single
bonds always stays the same.

Rule [2]: Two resonance structures must have the same number of
unpaired electrons.

27

Rule [3]: Resonance structures must be valid Lewis structures.
Hydrogen must have two electrons and no second-row element can
have more than eight.

28

• Curved arrow notation is a convention that is used to show how
electron position differs between the two resonance forms.
• Curved arrow notation shows the movement of an electron pair.
The tail of the arrow always begins at the electron pair, either in a
bond or lone pair. The head points to where the electron pair
―moves.‖
Example 1:

Example 2:

29

Resonance Structure Examples

In the two examples above, a lone pair is located on an
atom directly bonded to a double bond:
30

In the above examples, an atom bearing a (+) charge is
bonded either to a double bond or an atom with a lone
pair:

31

Resonance Hybrids
• A resonance hybrid is a composite of all possible
resonance structures. In the resonance hybrid, the
electron pairs drawn in different locations in individual
resonance forms are delocalized.
• When two resonance structures are different, the
hybrid looks more like the ―better‖ resonance
structure. The ―better‖ resonance structure is called
the major contributor to the hybrid, and all others are
minor contributors.
• The hybrid is a weighted average of the contributing
resonance structures.

32

A ―better‖ resonance structure is one that has more bonds and
fewer charges.

33

Isomer or resonance structure?

N

C

C

O

N

O

Isomer – same formula different
arrangement
O

O
HO

O

HO

O

Resonance – same formula and
arrangment

35

Draw the other resonance structure.
H2C

C
H

C
H
H2C

CH3

C
H

C
H

CH3

H2C

C
H

H
C

CH3

And the hybrid?
H2C

C
H

C
H

CH3

O

O

C
H3C

O
C

C

CH3

H3C

CH3

H3C

CH3

And the hybrid?
O
C
H3C

+
CH3

36

Determining Molecular Shape
Two variables define a molecule’s structure: bond length
and bond angle.

• Bond length decreases across a row of the periodic
table as the size of the atom decreases.

• Bond length increases down a column of the
periodic table as the size of an atom increases.

37

Determining Molecular Shape—Bond Angle
Bond angle determines the shape around any atom
bonded to two other atoms.

• The number of groups surrounding a particular atom
determines its geometry. A group is either an atom or a
lone pair of electrons.
• The most stable arrangement keeps these groups as
far away from each other as possible. This is
exemplified by Valence Shell Electron Pair Repulsion
(VSEPR) theory.

39

Two groups around an atom—

40

Three groups around an atom—

41

Four groups around an atom—

42

Drawing Three Dimensional Structures
• A solid line is used for a bond in the plane.
• A wedge is used for a bond in front of the plane.

• A dashed line is used for a bond behind the plane.

43

The molecule can be turned in many different ways,
generating many equivalent representations. All of the
following are acceptable drawings for CH4.

44

Note that wedges and dashes are used for groups
that are really aligned one behind another. It does not
matter in the following two drawings whether the
wedge or dash is skewed to the left or right, because
the two H atoms are really aligned.

45

A Nonbonded Pair of Electrons is Counted as a
―Group‖
In ammonia (NH3), one of the four groups attached to the
central N atom is a lone pair. The three H atoms and the
lone pair point to the corners of a tetrahedron. The H-N-H
bond angle of 107 is close to the theoretical tetrahedral
bond angle of 109.5 . This shape is referred to as a
trigonal pyramid.

46

In water (H2O), two of the four groups attached to the
central O atom are lone pairs. The two H atoms and
two lone pairs around O point to the corners of a
tetrahedron. The H-O-H bond angle of 105 is close to
the theoretical tetrahedral bond angle of 109.5 . Water
has a bent shape, because the two groups around
oxygen are lone pairs of electrons.

47

Methane (CH4)

Ammonia (NH3)

In both NH3 and H2O,
the bond angle is
smaller than the
theoretical tetrahedral
bond angle because of
repulsion of the lone
pairs of electrons. The
bonded atoms are
compressed into a
smaller space with a
smaller bond angle.

Water (H2O)
48

Predicting Geometry Based on Counting of Groups
Around the Central Atom
Figure 1.4
Summary: Determining
geometry based on the
number of groups

49

Predict the geometry of the following:
O

O

NH2

4 groups

Trigonal
planar

4 groups

tetrahedral

3 groups

tetrahedral

Predict the indicated angle.
O

Cl

120
H3C

Cl

H3C

H

109.5

H

50

Drawing Organic Molecules—Condensed Structures
• All atoms are drawn in, but the two-electron bond lines are generally
omitted.
• Atoms are usually drawn next to the atoms to which they are
bonded.
• Parentheses are used around similar groups bonded to the same
atom.
• Lone pairs are omitted.

51

Examples of Condensed Structures (from Figure 1.5)

52

Examples of Condensed Structures Containing a C-O
Double Bond (from Figure 1.6)

53

Skeletal Structures
• Assume there is a carbon atom at the junction of any two
lines or at the end of any line.
• Assume there are enough hydrogens around each carbon to
make it tetravalent.
• Draw in all heteroatoms and hydrogens directly bonded to
them.

54

Examples of Skeletal Structures (from Figure 1.7)

55

Words of Caution Regarding Interpretation of Skeletal
Structures…
• A charge on a carbon atom takes the place of one hydrogen
atom.
• The charge determines the number of lone pairs. Negatively
charged carbon atoms have one lone pair and positively
charged carbon atoms have none.

56

Convert to a Lewis structure
H

CO2CH3

O

H

O

CH3

N
H

N

H

Convert to a condensed structure.

OH

CH3CH3C(CH3)2CH2OH

57

Orbitals and Bonding: Hydrogen
When the 1s orbital of one H atom overlaps with the 1s
orbital of another H atom, a sigma ( ) bond that
concentrates electron density between the two nuclei is
formed.

This bond is cylindrically symmetrical because the
electrons forming the bond are distributed symmetrically
about an imaginary line connecting the two nuclei.

58

Orbitals and Bonding: Methane
To account for the bonding patterns observed in more
complex molecules, we must take a closer look at the 2s and
2p orbitals of atoms in the second row.
Carbon has two core electrons, plus four valence electrons. To
fill atomic orbitals in the most stable arrangement, electrons
are placed in the orbitals of lowest energy. For carbon, this
places two in the 2s orbital and one each in 2p orbitals.

Note: The lowest energy arrangement of electrons for an atom is called its
59
ground state.

In this description, carbon should form only two bonds
because it has only two unpaired valence electrons, and
CH2 should be a stable molecule. However, CH2 is a very
unstable species that cannot be isolated under typical
laboratory conditions. Note that in CH2, carbon would not
have an octet of electrons.

60

There is a second possibility. Promotion of an electron from a
2s to a vacant 2p orbital would form four unpaired electrons
for bonding. This process requires energy because it moves
an electron to a higher energy orbital. This higher energy
electron configuration is called an electronically excited state.

But this description is still not adequate. Carbon would form
two different types of bonds: three with 2p orbitals and one
with a 2s orbital. However, experimental evidence points to
carbon forming four identical bonds in methane.
61

To solve this dilemma, chemists have proposed that atoms
like carbon do not use pure s and pure p orbitals in forming
bonds. Instead, atoms use a set of new orbitals called hybrid
orbitals.
Hybridization is the combination of two or more atomic
orbitals to form the same number of hybrid orbitals, each
having the same shape and energy.

62

Shape and Orientation of sp3 Hybrid Orbitals
The mixing of a spherical 2s orbital and three dumbbell
shaped 2p orbitals together produces four hybrid orbitals,
each having one large lobe and one small lobe (Figure 1.8).

The four hybrid orbitals are oriented towards the corners of a
tetrahedron, and form four equivalent bonds.

63

Bonding Using sp3 Hybrid Orbitals
Each bond in CH4 is formed by overlap of an sp3 hybrid
orbital of carbon with a 1s orbital of hydrogen. These
four bonds point to the corners of a tetrahedron.
Figure 1.9
Bonding in CH4 using sp3
hybrid orbitals

64

Other Hybridization Patterns
• One 2s orbital and three 2p orbitals form four sp3 hybrid
orbitals.
• One 2s orbital and two 2p orbitals form three sp2 hybrid
orbitals.
• One 2s orbital and one 2p orbital form two sp hybrid orbitals.

65

To determine the hybridization of an atom in a molecule,
we count the number of groups around the atom. The
number of groups (atoms and nonbonded electron pairs)
corresponds to the number of atomic orbitals that must
be hybridized to form the hybrid orbitals.

66

Hybridization Examples

Figure 1.12
Hybrid orbitals of NH3 and
H2O

67

Determine the type of orbitals that make up each bond in
each molecule.
C-H Csp3 with Hs
HC
Be
H
3

C-Be Csp3 with Besp

Be-H Besp with Hs

H3C

CH3
B

C-H Csp3 with Hs
C-B Csp3 with Bsp2

CH3

68

Hybridization and Bonding in Organic Molecules

69

Making a model of ethane illustrates one
additional feature about its structure.
Rotation occurs around the central C—C
bond.

70

Each carbon is trigonal and
planar.
Each carbon is sp2 hybridized

71

Unlike the C—C bond in ethane, rotation about the C—C
double bond in ethylene is restricted. It can only occur if the
bond first breaks and then reforms, a process that requires
considerable energy.

73

Each carbon atom has two
unhybridized 2p orbitals that
are perpendicular to each
other and to the sp hybrid
orbitals. The side-by-side
overlap of two 2p orbitals on
one carbon with two 2p
orbitals on the other carbon
creates the second and third
bonds of the triple bond. All
triple bonds are composed of
one sigma and two pi bonds.

76

From Figure 1.14

Summary of Bonding in Acetylene

77

Summary of Covalent Bonding Seen in Carbon Compounds
(from Figure 1.15)

78

Determine the hybridization of each atom in the
indicated bond.
N

Both the C and N have 3
groups around them so
they are sp2.

Classify each bond as σ or π.
O

H3C

C-CH3 and C-H are σ bonds.
H

C=O is made up of a σ and π
bond.

79

Bond Length and Bond Strength
• As the number of electrons between two nuclei
increases, bonds become shorter and stronger.

• Thus, triple bonds are shorter and stronger than
double bonds, which are shorter and stronger than
single bonds.

80

• The length and strength of C—H bonds vary depending
on the hybridization of the carbon atom.

81

Note:
• As the percent s-character increases, a hybrid orbital holds
its electrons closer to the nucleus, and the bond becomes
shorter and stronger.
• Although sp3, sp2 and sp hybrid orbitals are similar in
shape, they are different in size.

84

Which of the indicated bonds is the shortest?
a
b
c

B, the triple bond is the shortest.
Which C-H bond is the shortest?
H
H

a

b

A has 50% s character, due to it being made up of
an sp hybridized bond, and is thus shorter.
85

Electronegativity and Bond Polarity
Electronegativity is a measure of an atom’s attraction for
electrons in a bond.
Electronegativity values for some common elements:

86

Electronegativity values are used as a guideline to indicate whether
the electrons in a bond are equally shared or unequally shared
between two atoms. When electrons are equally shared, the bond is
nonpolar. When differences in electronegativity result in unequal
sharing of electrons, the bond is polar, and is said to have a
―separation of charge‖ or a ―dipole‖.

• A carbon—carbon bond is nonpolar. The same is true whenever
two different atoms having similar electronegativities are bonded
together.
• C—H bonds are considered to be nonpolar because the
87
electronegativity difference between C and H is small.

Bonding between atoms of different electronegativity values results in
unequal sharing of electrons.
Example: In the C—O bond, the electrons are pulled away from C (2.5)
toward O (3.4), the element of higher electronegativity. The bond is
polar, or polar covalent. The bond is said to have dipole; that is,
separation of charge.
+

means the
indicated atom is
electron deficient.
- means the

indicated atom is
electron rich.
The direction of polarity in a bond is indicated by an arrow with the
head of the arrow pointing towards the more electronegative element.
The tail of the arrow, with a perpendicular line drawn through it, is
drawn at the less electronegative element.
88

Polarity of Molecules
Use the following two-step procedure to determine if a
molecule has a net dipole:
1. Use electronegativity differences to identify all of the
polar bonds and the directions of the bond dipoles.
2. Determine the geometry around individual atoms by
counting groups, and decide if individual dipoles cancel
or reinforce each other in space.
Electrostatic potential plot of CH3Cl

89

A polar molecule has either one polar bond, or two or more
bond dipoles that reinforce each other. An example is water:

A nonpolar molecule has either no polar bonds, or two or
more bond dipoles that cancel. An example is carbon dioxide:

90

Label the most electronegative and electropositive in
the group of atoms below:
O
Most EN

C

Be
Most EP

Draw an arrow showing the direction of the dipole
in the indicated bond.
Cl

The dipole goes from C, which has a
partial positive charge, to Cl, which has
a partial negative charge.
91

Which of the following is polar due to it having a
net dipole.
Cl

Cl
Cl

H

H

Cl

H

H

Cl

H

H

Cl

Cl

H

H

Cl

92

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