Molecular
Structures
Chemistry: The Molecular Science, 3rd Ed.
by Moore, Stanitski, and Jurs
1
Molecular Structure
Molecular geometry is the
general shape of a molecule or the
arrangement of atoms in three
dimensional space.
Physical and chemical properties
depend on the geometry of a
molecule.
2
Molecular Structures
3-D Model
3-D Drawing
3
Does it matter?
The Thalidomide Story

The chemical structure of thalidomide.
models – enantiomers (mirror image)
“The Same and Not the Same”, by Roald Hoffmann
1995, Columbia University Press
4
Does it matter?
Fatty Acids
‘trans’ fatty acid
‘cis’ fatty acid
5
VSEPR Model
The Valence Shell Electron Pair Repulsion model
predicts the shapes of molecules and ions by
assuming that the valence shell electron pairs are
arranged as far from one another as possible to
minimize the repulsion between them.
6
VSEPR Model
H
N
:
H
H
Electron Pair Geometry –
is determined by the number and
arrangement of all electron pairs
(bonding and lone) around the
central atom.
Molecular geometry –
is determined by the arrangement of
atoms (or bonding electron pairs
only) around the central atom.
In molecules with no lone pairs,
Electron Pair Geometry = Molecular Geometry
7
Fig. 9-4, p.383
AX3E0
AXE shorthand notation:
• A - central atom
• X - terminal atoms
• E - lone pair electrons
8
Predicting Molecular
Geometry: VSEPR


# e- pairs
Only five basic shapes.
When a lone pair replaces an atom, the molecular
geometry changes as well as the angles.
2
3
4
5
6
Fig. 9-4, p.383 9
Predicting Molecular
Geometry: VSEPR
1. Draw the Lewis structure.
2. Determine how many electron pairs (bonded and non-bonded) are
around the central atom. **Treat a multiple bond like a single
bond when determining a shape.
3. Write the AXE shorthand notation.
4. Determine the electron pair geometry (**one of the five basic
shapes).
5. If the molecule has lone pairs around the central atom, then
determine the molecular geometry. (This is a subset of the
electron geometry.)
10
Linear (Electron Geometry)
Two e- pairs about central atom
lone
pairs
2
0
1
1-3
Molecular
Geometry
linear
..
bond
pairs
linear
The molecular geometry here is the same as the electronic
geometry even though there is a lone pair. ‘Two points make a line.’
11
Predicting Molecular Geometry
Example 1: BeCl2
1. Draw the Lewis structure
Cl
Be
AX2E0
Cl
2. Two electron pairs around the
central atom.
Two bonded and Zero lone pairs.
electron pair geometry = molecular geometry
Geometry is Linear. Bond angle is 180o.
12
Trigonal Planar (Electron Geometry)
Three e- pairs about central atom
bond
pairs
Molecular
Geometry
0
triangular planar
2
1
angular (bent)
1
2
..
..
3
lone
pairs
Model
linear
13
Predicting Molecular Geometry
Example 2: BF3
..
:F:
..
:F
..
B
AX3E0
..
F:
..
Three electron pairs around the
central atom.
Three bonded and Zero lone pairs.
triangular planar
(or trigonal planar)
14
Predicting Molecular Geometry
Example 3: SO2
AX3E0
O
S
AX2E1
O
Three electron pairs around the
central atom.
Two bonded and One lone pairs.
S
electron geometry = triangular planar.
molecular geometry = bent or angular.
O
O
15
Tetrahedral (Electron Geometry)
Four e- pairs about central atom
bond
pairs
lone
pairs
4
0
3
1
2
2
tetrahedral
Model
..
triangular
pyramidal
..
angular
(bent)
16
Predicting Molecular Geometry
Example 4: CH4
AX4E0
H
H
C
H
H
Four electron pairs around the
central atom. Zero lone
pairs.
tetrahedral
electron pair geometry = molecular geometry
17
Predicting Molecular Geometry
Example 5: NH3
H
N
H
AX4E0
AX3E1
H
Four electron pairs around the
central atom.
Three bonded and One lone pair.
N
H
electron geometry = tetrahedral.
H
molecular geometry = triangular pyramidal H
18
Predicting Molecular Geometry
Example 6: H2O
AX4E0
H
O
AX2E2
H
Four electron pairs around the
central atom.
Two bonded and Two lone pairs.
O
electron geometry = tetrahedral
molecular geometry = angular or bent
H
H
19
Predicting Molecular Geometry
Tetrahedral - bond angles
Order of increasing repulsion:
bonding pair-bonding pair
<
bonding pair-lone pair
<
lone pair-lone pair
20
Trigonal Bipyramidal (Electron Geometry)
Five e- pairs about central atom
..
90°
..
..
120°
Triangular bipyramidal
Seesaw
The atoms are non-equivalent.
Green atoms are axial;
blue atoms are equatorial.
T-shaped
Linear
**Put lone pairs
in the equatorial
positions.
21
Predicting Molecular Geometry
Example 7: PF5
:
: :
:F
P
F:
F:
:
:F:
: : : :
:F:
AX5E0
Five electron pairs around the
central atom.
electron and molecular geometry=
Zero lone pairs.
trigonal bipyramidal
22
Predicting Molecular Geometry
Example 8: SF4
:
: :: :
:F
AX5E0
AX4E1
:
:F
S:
:F
:F :
Five electron pairs around the
central atom.
Four bonded and One lone pair.
electron geometry = trigonal bipyramidal
molecular geometry = seesaw
23
Predicting Molecular Geometry
Example 9: BrF3
:
:F :
AX5E0
AX3E2
: :
Br F:
:
:F :
Five electron pairs around the
central atom.
Three bonded and Two lone pairs.
electron geometry = trigonal bipyramidal
molecular geometry = T-shaped
24
Predicting Molecular Geometry
Example 10: XeF2
:
AX5E0
:F :
AX2E3
Xe :
:
:F :
Five electron pairs around the
central atom.
Two bonded and Three lone pairs.
electron geometry = trigonal bipyramidal
molecular geometry = linear
25
Octahedral (Electron Geometry)
Six e- pairs about central atom
90°
Octahedral
Square pyramid
Square planar
Equivalent atoms
26
Predicting Molecular Geometry
Example 11: SF6
:
S
: :
: :
:
:
:F
:F:
F:
:
F:
:
:F
AX6E0
:
:F:
Six electron pairs around the central atom.
Six bonded and Zero lone pairs.
electron geometry = octahedral
molecular geometry = octahedral
27
Predicting Molecular Geometry
Example 12: IF5
:
AX6E0
:F
:F
I
AX5E1
: :: :
: :: :
:
:F :
F:
F:
Six electron pairs around the
central atom.
Five bonded and Two lone pairs.
electron geometry = octahedral
molecular geometry = square pyramidal
28
Predicting Molecular Geometry
: :: :
AX6E0
AX5E1
:
:
: :: :
: :
Example 13: XeF4
:
:
F
F
Xe
F
F
Six electron pairs around the
central atom.
Four bonded and Two lone pairs.
electron geometry = octahedral
molecular geometry = square planar
29
Predicting Molecular Geometry
Fig. 9-5, p.391
30
Predicting Molecular Geometry
Fig. 9-6, p.393
31
Practice






ICl
ICl3
ICl5
GeF4
SeF4
XeF4



CO2
SO2
ClO2-
32
Bond Angles
CHO
Give the approximate
values for the indicated
bond angles.
COH
OCN
HNH
33
Molecular Geometry
Dipole Moment and Polarity
Electronegativity (EN) values are used to predict the polarity of
covalent bonds. The greater EN, the more polar will be the
bond. A polar bond has a dipole or slight separation of charge
(from the unequal sharing of bond electrons). [Chapter 8]
The polarity of a molecule depends on the sum of all the bond
dipoles (vectors). If there is a net dipole for the molecule, than
the molecule is polar. A molecule that has polar bonds may or
may not be polar.
The dipole moment (μ) is a measure of the degree of charge
separation or the polarity.
34
Molecular Geometry
Dipole Moment and Polarity
d-
d+
d-
O
C
O
nonpolar, bp=-79C
dipole moment, μ = 0 D
d-
O
polar, bp=100C
d+
H
H d+
+
Net
dipole
dipole moment, μ = 1.85 D
35
Molecular Geometry
Dipole Moment and Polarity
In general, a molecule is polar if:


it isn’t a basic VSEPR shape (symmetrical)
Ex: H2O, bent (polar)
or if the terminal atoms/groups in a
basic VSEPR shape differ.
Ex: CH2Cl2, tetrahedral (polar)
36
Dipole Moment and Molecular
Geometry
Molecules that exhibit any asymmetry in the
distribution of electrons would have a nonzero net
dipole moment. These molecules are considered
polar.
Non polar
Polar
VSEPR shape
identical atoms
VSEPR shape
atoms differ
37
Dipole Moment and Molecular
Geometry
38
Molecular Geometry
Dipole Moment and Polarity
Non polar
+
PF3Cl2
PF5
Non polar
VSEPR shape
identical atoms
Atoms differ. BUT can
be divided into
nonpolar VSEPR
shapes:
linear + triangular
planar
PF4Cl
Polar
Polar
Atoms differ. Doesn’t
divide into nonpolar
VSEPR shapes
VSEPR
shape
atoms differ
PF3Cl2
39
Dipole Moment and Molecular
Geometry
F
Cl
ClF3
F
T-shaped
No symmetry → polar
F
F
XeF4
F
..
Xe
..
F
F
S:
F
F
F
F
F
Xe:
Square Planar
Symmetric → non polar
SF4
SeeSaw
No symmetry → polar
XeF2
Linear
Symmetric → non polar
F
40
Molecular Geometry
Dipole Moment and Polarity
CO, PCl3, BCl3, GeH4, CF4

Which compound is the most polar?

Which compounds on the list are non-polar?
41
Orbitals Consistent with
Molecular Shape
Lewis dot + VSEPR gives the correct
shape for a molecule. BUT…
How do atomic orbitals (s, p, d …) produce
these shapes?
Valence bond theory describes a bond as an
overlap of atomic (hybrid) orbitals.
42
Valence Bond Model
H
F
H2
1s
2s
2px 2py 2pz
HF
43
Valence Bond Theory
…and, why do we draw
the Lewis structures like
we do?
This works for H2 and HF, but…
 Why does Be form compounds?


no unpaired electrons
Be
[He] 2s2
2s
Why does C form 4 equivalent bonds at tetrahedral angles?


only two unpaired electrons
p orbitals are at 90° to each other (not 109.5°)
C [He]2s22p2
2s
2px 2py 2pz
44
Orbitals Consistent with
Molecular Shapes

Atomic orbitals (AOs) can be hybridized (mixed).
• Sets of identical hybrid orbitals form identical
bonds.
• # AOs that hybridize = # hybrids orbitals .
s+p
sp + sp
s+p+p
sp2 + sp2 + sp2
etc….
45
sp Hybrid Orbitals
Energy, E
AX2E0, Ex: BeCl2,
2p 2p 2p
2p 2p 2p
Promotion
Two unhybridized
p orbitals
Orbital
hybridization
2s
2s
Two sp hybrid
orbitals on Be in BeF2
Isolated Be atom
sp hybridization occurs around the central atom whenever there
are two regions of high e- density.
Two equivalent covalent bonds form (180° apart) LINEAR.
46
sp Hybrid Orbitals
47
sp2 Hybrid Orbitals
AX3E0, Ex: BF3
The result is THREE equivalent
hybrid orbitals, in a VSEPR basic
shape of trigonal planar.
48
p. 396
sp3 Hybrid Orbitals
AX4E0, Ex: CH4
TETRAHEDRAL
49
sp3 Hybrid Orbitals
AX3E1 ( NH3)
and
AX2E3 ( H2O)
50
Orbitals Consistent with
Molecular Shapes
Describe bonding in PCl5 using hybrid orbitals.
:
:
P
: :
:
: Cl :
Cl:
:
: Cl
Cl :
trigonal bipyramidal
We need 5 orbitals.
:
:
:Cl :
AX5E0
51
sp3d Hybrid Orbitals
3d
valence
shell
hybridization
3p
five equal sp3d
hybrid orbitals
X
3s
P atom (ground state)
52
sp3d Hybrid Orbitals
3d
sp3d
P atom (hybridized state)
53
Orbitals Consistent with
Molecular Shapes
Describe the bonding in SF6 using hybrid orbitals.
:
:
:
:F
:F:
F:
:F
: :
: :
S
F:
AX6E0
Octahedral
We need 6 orbitals.
:
:
: F:
:
54
sp3d 2 Hybrid Orbitals
3d
X
hybridization
3p
six equal sp3d2
hybrid orbitals
X
3s
S atom (ground state)
55
sp3d 2 Hybrid Orbitals
3d
sp3d2
S atom (hybridized state)
56
Summary - Hybrid Orbitals
Hybrid
Orbital
Geometric
Arrangements
Number of
Orbitals
Example
sp
Linear
2
Be in BeF2
sp2
Trigonal planar
3
B in BF3
sp3
Tetrahedral
4
C in CH4
sp3d
Trigonal bipyramidal
5
P in PCl5
sp3d2
Octahedral
6
S in SF6
57
Hybridization
Mixed
s+p
s+p+p
s+p+p+p
Hybrids (#) Remaining
sp (2)
p+p
sp2 (3)
p
sp3 (4)
Geometry
Linear
Triangular planar
Tetrahedral
Mixed
Hybrids (#) Remaining
Geometry
s+p+p+p+d
sp3d (5)
d+d+d+d
Triangular bipyramid
d+d+d
Octahedral
s+p+p+p+d+d sp3d2 (6)
58
Practice
What are the
hybridization and
approximate bond
angles for each C, N, O
in the given molecules?
59
What about…
multiple bonding!
According to valence bond theory hybrid orbitals
include:



single bonds
lone pairs
one of the bonds in a multiple bond.
The electrons in the unhybridized atomic orbitals
are used to form the additional multiple
bonds.
60
Multiple Bonding
• A s (sigma) bond is an overlap of orbitals
(hybrids) along the bond axis.
• A p (pi) bond is a overlap of parallel “p” orbitals,
creating an electron distribution above and below
the bond axis.
61
Multiple Bonding
(unhybridized)
2p
2p
Energy
sp2
2s
1s
C atom (ground state)
1s
(3 sp2 hybrid
+ 1 unhybridized p)
62
Multiple Bonding
2p
2p
(unhybridized)
Energy
sp2
2s
1s
O atom (ground state)
1s
(3 sp2 hybrid +
1 unhybridized p)
63
Multiple Bonding
σ
π
64
Multiple Bonding
65
Multiple Bonding
66
Practice
σ

Identify the pi and sigma
bonds in the given
molecules.
σ
σ
π
σ
σ
σ
π, π
67
Types of Intermolecular
Forces
δ+
δ-
δ+
δ-
Intermolecular Interactions
London Forces
(0.05 – 40 kJ/mol)
Dipole-Dipole Forces
(5 – 25 kJ/mol)
Hydrogen Bonding
(10 – 40 kJ/mol)
(Intramolecular Covalent Bond
150 – 1000 kJ/mol)
68
Types of Intermolecular
Forces
London Forces
(dispersion forces)
When electrons are momentarily
unevenly distributed in the molecule,
polarization occurs.
Induced Dipole
All molecules, EVEN nonpolar ones experience London Forces!
(Nonpolar molecules do not experience any other intermolecular interaction)
69
Types of Intermolecular
Forces
To boil (l g), molecules must
have enough energy to
overcome their intermolecular
forces.
The higher the intermolecular
force …the higher the boiling
point!
Dispersion Forces increase with increased number of electrons.
increased
polarizability
70
Types of Intermolecular
Forces
A polar molecule is a
Permanent Dipole that
creates ….
Dipole-Dipole forces
71
Types of Intermolecular
Forces
The more polar the molecule
(at a given size) …
… the higher the boiling
point!
72
Types of Intermolecular
Forces
Hydrogen bond
…is established by the attraction between hydrogen and an
electron pair on a small, very electronegative atom.
+δ
X—H
- - - :Z—
X = N, O, F
Z = N, O, F
This bond is responsible of determining the three dimensional
structure of large proteins molecules
73
Types of Intermolecular
Forces
Water:
One molecule can participate in four
H bonds with other molecules.
Because of the hydrogen bond, water
has a boiling point 200 C higher than
if the bond were not present.
74
Practice

Explain the following boiling points,


Which of the following will form H-bonds:


HF (20˚C), HCl (-80˚C), HBr (-60˚C), HI (-25˚C)
CH2Br2, CH3OCH2CH3, CH3CH2OH, H2NCH2COOH
What types of forces must be overcome in these
changes?



The sublimation of solid C10H8
The decomposition of water into H2 and O2
The evaporation of PCl3
75