Molecular Structures
Two C2H6O structural isomers:
H H
|
| ..
H – C – C – ..
O–H
|
|
H H
H
H
| .. |
H – C – ..
O–C–H
|
|
H
H
dimethyl ether
ethanol
Chapter 9: Molecular Structures
m.p./ °C
b.p./ °C
-114.1
78.3
-141.5
-24.8
Molecular shape is important!
Small structural changes cause large changes in
physical (and chemical) properties.
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© 2008 Brooks/Cole
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Using Molecular Models
Using Molecular Models
Physical models of 3D-structures:
Hand-drawn molecules:
Going back into
the screen
ball and stick
space filling
C
H
Computer versions:
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H
In the plane of
the screen
H
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Predicting Molecular Shapes: VSEPR
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Predicting Molecular Shapes: VSEPR
1.  e- pairs stay as far apart as possible to minimize
repulsions.
2.  The shape of a molecule is governed by the
number of bonds and lone pairs present.
3.  Treat a multiple bond like a single bond when
determining a shape. Each is a single e-group.
4.  Lone pairs occupy more volume than bonds.
Linear
Triangular planar
Triangular bipyramidal
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H
Coming out of
the screen
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Tetrahedral
Octahedral
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Predicting Molecular Shapes: VSEPR
Predicting Molecular Shapes: VSEPR
Basic shapes that minimize repulsions:
A molecule may be described by its:
•  electron-pair (e-pair) geometry
•  molecular geometry
triangular
planar
linear
tetrahedral
triangular
bipyramidal
octahedral
These two geometries may be different.
If the molecule contains:
•  Atoms can be “seen”, lone pairs are invisible.
•  only bonding pairs – the angles shown are correct.
•  lone pair/bond mixtures – the angles change a little.
  lone pair/lone pair repulsions are largest.
  lone pair/bond pair are intermediate in strength.
  bond/bond interactions are the smallest.
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Predicting Molecular Shapes: VSEPR
Predicting Molecular Shapes: VSEPR
2 and 3 e-group central atoms
2 e-groups:
Triangular planar e-pair
geometry
Linear e-pair
geometry
2 e-groups
bond
pairs
lone
pairs
0
3
linear
180.0°
0
O C
triangular planar
2
1
angular (bent)
linear
1
molecular geometry
2
“2” bonds, 0 lone pairs on C.
(treat double bonds as 1 bond)
Linear.
O
..
1
..
1
2 bonds, 0 lone pairs on Be.
Linear.
lone
pairs
180.0°
H C C
..
2
Cl Be Cl
3 e-groups
..
bond
pairs
180.0°
linear
Each C has 2 e-groups.
Each H-C-C unit is linear.
H
180.0°
molecular geometry
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Predicting Molecular Shapes: VSEPR
Predicting Molecular Shapes: VSEPR
3 e-groups:
4 e-groups = tetrahedral e-pair geometry:
120°
Cl
B has 3 bonds (0 lone pairs).
Triangular planar.
0
tetrahedral
3
C
C H
H
H
Each C has 3 e-groups.
Each C is triangular planar.
..
H
1
triangular
pyramidal
2
2
angular
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1 bond, 3 lone pairs?
..
Cl
lone
pairs
4
..
Cl B
bond
pairs
All molecules with only 1
bond are linear!
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2
Predicting Molecular Shapes: VSEPR
H
109.5°
Predicting Molecular Shapes: VSEPR
VSEPR applies to each atom in a molecule.
•  Alkanes: each C is tetrahedral.
4 bonds, 0 lone pairs.
All angles = tetrahedral angle
H C H
H
3 bonds, 1 lone pair.
Lone-pair/bond > bond/bond repulsion
H-N-H angle is reduced.
..
H N H
H
107.5°
..
2 bonds, 2 lone pairs.
Two lone pairs
H-O-H angle even smaller.
H
..
H O
104.5°
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Predicting Molecular Shapes: VSEPR
Predicting Molecular Shapes: VSEPR
Lactic acid:
Expanded octet atoms:
Tetrahedral O
H
O
C
C
C
H
H
O
..
O
..
..
..
H
..
..
H
Triangular planar C
H
Tetrahedral C
Tetrahedral C
Tetrahedral O
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Predicting Molecular Shapes: VSEPR
bond
pairs
5
4
3
2
lone
pairs
0
1
2
3
6
5
4
3
0
1
2
3
..
..
..
..
Octahedral
Square pyramidal
Square planar
T-shaped
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F
..
Remember
•  lone pairs
repel the most.
•  they get as far
apart as
possible.
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Predicting Molecular Shapes: VSEPR
90°
..
Shape
Triangular bipyramidal
Seesaw
T-shaped
Linear
F
F
F P F
F S F
F Cl F
F
F
F
F Xe F
T-shaped
Linear
PF5
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..
..
..
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© 2008 Brooks/Cole
SF4
ClF3
..
Seesaw
..
Triangular bipyramidal
..
120°
XeF2
18
3
Predicting Molecular Shapes: VSEPR
Predicting Molecular Shapes: VSEPR
Six e-groups = octahedral e-pair geometry
F
90°
F
F
F S F
..
F
F
F
F Br F
F
F
F Xe F
F
90°
..
Square pyramid
..
Octahedral
Square planar
Equivalent atoms
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Orbitals Consistent with Molecular Shapes
XeF4
BrF5
SF6
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Orbitals Consistent with Molecular Shapes
VB theory: bonds occur when atomic orbitals overlap.
H2 – H(1s) overlaps H(1s)
HF – H(1s) overlaps F(2p)
How do atomic orbitals (s, p, d …) produce these
shapes?
74 pm
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Valence Bond Theory
109 pm
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Orbitals Consistent with Molecular Shapes
This works for H2 and HF, but…
•  Why does Be form compounds?
  Be (1s2 2s2)
  No unpaired e- to share.
  Experiments show: linear BeH2, BeCl2, …
One s orbital + one p orbital → two sp hybrids.
•  Why does C form 4 bonds at tetrahedral angles?
 
 
 
 
C (1s2 2s2 2p2)
2px1 2py1 Two bonds?
p orbitals are at 90° to each other
Experiments show: tetrahedral CH4, CCl4, …
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4
sp Hybrid Orbitals
sp2 Hybrid Orbitals
Be compounds (BeH2, BeF2 …):
B forms three sp2 hybrid orbitals:
Energy, E
2p 2p 2p
Two unhybridized
p orbitals
2p 2p 2p
Promotion
  One s orbital mixes with two p orbitals.
  One p orbital is unmixed.
Orbital
hybridization
Two sp hybrid
orbitals on Be in BeF2
2s
Isolated Be atom
2s
Each sp hybrid (180° apart) holds one e-.
Two equivalent covalent bonds form.
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© 2008 Brooks/Cole
sp2 Hybrid Orbitals
sp3 Hybrid Orbitals
B compounds (BH3, BF3 …):
C forms four sp3 hybrid orbitals:
Energy, E
2p 2p 2p
Promotion
  One s orbital mixes with three p orbitals.
  All p orbitals are mixed.
One unhybridized
and vacant p orbital
2p 2p 2p
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Orbital
hybridization
Three sp2 hybrid
orbitals of B in BF3
2s
Isolated B atom
2s
Each sp2 hybrid (120° apart) holds one e-.
Three equivalent covalent bonds form.
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In C, each sp3 hybrid (109.5° apart) holds one e-.
Four equivalent covalent bonds form.
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sp3 Hybrid Orbitals
sp3 Hybrid Orbitals
N and O compounds (NH3, H2O…) have more e-:
“Octet rule” molecules have tetrahedral e-pair shape.
•  sp3 hybridized (CH4, NH3, H2O, H2S, PH3, …)
H
σ bond
C
H
H
H
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5
Hybridization in Expanded Octets
Hybridization in Molecules with Multiple Bonds
Summary:
A carbon atom can have a:
•  tetrahedral center (CH4, CHF3 , C2H6…) = sp3
•  triangular-planar center (H2CO, C2H4 …) = sp2
Mixed
s+p
s+p+p
s+p+p+p
Hybrids (#) Remaining Geometry
sp (2)
p+p
Linear
sp2 (3)
p
Triangular planar
sp3 (4)
Tetrahedral
H
C
C H
H
H
d orbitals can also form hybrids:
Mixed
Hybrids (#) Remaining Geometry
s+p+p+p+d
sp3d (5)
d+d+d+d
Triangular bipyramid
s+p+p+p+d+d
sp3d2 (6)
d+d+d
Octahedral
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Hybridization in Molecules with Multiple Bonds
Formaldehyde is similar:
H
C
32
Hybridization in Molecules with Multiple Bonds
H
C (sp2) + C (sp2) overlap (σ bond):
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C
H
H
Unhybridized C p orbitals each contain one e-.
H
C σ bond C
H
H
C
overlap
H
C
H
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H
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Hybridization in Molecules with Multiple Bonds
Hybridization in Molecules with Multiple Bonds
A third type of C center is seen:
σ bond: C (sp) + C (sp) overlap:
  linear center (C2H2, acetylene) = sp hybridized
H
C
C
H
C
C H
H
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H
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© 2008 Brooks/Cole
C
C
H
overlap
H
C
C
H
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6
Molecular Polarity
Hybridization in Molecules with Multiple Bonds
π bonds prevent bond rotation:
O = C = O
δ-
δ-
•  The dipoles cancel because of CO2’s shape.
Non-rotating double bonds allow cis-trans isomerism
to occur.
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2δ+
the arrow points to δ-,
the + shows δ+
•  the bond dipoles have equal size but point in opposite
directions.
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Molecular Polarity
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Molecular Polarity
Molecule
H2
0
HF
HCl
HBr
HI
H 2O
H 2S
CO2
CH4
CH3Cl
CH2Cl2
CHCl3
CCl4
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Molecular Polarity
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µ (D)
1.78
1.07
0.79
0.38
1.85
0.95
0
0
1.92
1.60
1.04
0
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Molecular Polarity
•  Polar molecules: bond dipoles do not cancel
•  Water is polar:
.. ..
O
H
H
+
Net
dipole
Observed dipole, µ = 1.85 D
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Molecular Polarity
Molecular Polarity
H
F
C
F
F
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Molecular Polarity
C
F
F
F
F
Net
dipole
CHF3 is polar
CF4 is non polar
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+
No net dipole
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Noncovalent Interactions
Molecules are sticky and attract each other.
+
PF3Cl2
PF5
+
PF4Cl
PF3Cl2
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London Forces
δ+
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London Forces
δ-
δ+
Atom Molecule
He
Ne
Ar
Kr
F2
Cl2
Br2
I2
CH4
C 2H 6
C 3H 8
C4H10
δ-
•  Strength (0.05 ↔ 40 kJ/mol):
Small molecule = few e- = weak attraction.
Large molecule = many e- = stronger attraction.
•  The only force between nonpolar molecules.
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© 2008 Brooks/Cole
# of e2
10
18
36
18
34
70
106
10
18
26
34
bp (°C)
−269
−246
−186
−152
−188
−34
+59
+184
−161
−88
−42
0
More e= larger attraction
= greater stickiness
= higher b.p.
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8
Dipole-Dipole Attractions
Dipole-Dipole Attractions
Polar molecules attract each
other.
nonpolar
SiH4
GeH4
Br2
bp (°C)
−112
−90
+59
polar
PH3
AsH3
ICl
# of e18
36
70
bp (°C)
−88
−62
+97
With equal number of e- (and same shape):
dipole/dipole > London
Strength = 5 ↔ 25 kJ/mol.
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# of e18
36
70
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Hydrogen Bonds
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Hydrogen Bonds
An especially large dipole-dipole attraction.
  10 ↔ 40 kJ/mol
  Occurs when H bonds directly to F, O or N
H on one molecule
interacts with O on
another molecule.
F, O & N are small with large electronegativities.
  results in large δ+ and δ- values.
H-bonds are usually drawn as dotted lines.
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Hydrogen Bonds
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Noncovalent Forces in Living Cells
Phospholipids form lipid bilayers:
Water is a liquid at room
T (not a gas).
Polar end = hydrophilic (water loving).
Nonpolar end = hydrophobic (water hating).
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9
Biomolecules: DNA and Molecular Structure
Biomolecules: DNA and Molecular Structure
In DNA there are 4 possible bases—adenine (A), thymine (T), guanine (G),
or cytosine (C)
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Biomolecules: DNA and Molecular Structure
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Biomolecules: DNA and Molecular Structure
Complementary base pairs:
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