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© 2008 Brooks/Cole 1
Chapter 9: Molecular Structures
© 2008 Brooks/Cole 2
Molecular Structures
dimethyl ether
H – C – O – C – H
H |
| H
H |
| H
..
..
ethanol
H – C – C – O – H
H |
| H
H |
| H
..
..
Two C2H6O structural isomers:
Molecular shape is important! Small structural changes cause large changes in physical (and chemical) properties.
m.p./ °C -114.1 -141.5 b.p./ °C 78.3 -24.8
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Physical models of 3D-structures:
ball and stick space filling
Computer versions:
Using Molecular Models
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Hand-drawn molecules:
H
C H H
H In the plane of
the screen
Going back into the screen
Coming out of the screen
Using Molecular Models
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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.
Predicting Molecular Shapes: VSEPR
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Predicting Molecular Shapes: VSEPR
Linear Triangular planar Tetrahedral
Triangular bipyramidal Octahedral
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Basic shapes that minimize repulsions:
If the molecule contains: •! 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.
linear triangular planar
tetrahedral triangular bipyramidal
octahedral
Predicting Molecular Shapes: VSEPR
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A molecule may be described by its: •! electron-pair (e-pair) geometry •! molecular geometry
These two geometries may be different.
•! Atoms can be “seen”, lone pairs are invisible.
Predicting Molecular Shapes: VSEPR
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3 e-groups bond lone pairs pairs
2 and 3 e-group central atoms
.. ..
.. ..
.. ..
2 e-groups bond lone pairs pairs 2 0 linear
.. .. 1 1 linear
3 0 triangular planar
2 1 angular (bent)
1 2
linear
Triangular planar e-pair geometry
molecular geometry
Linear e-pair geometry
molecular geometry
Predicting Molecular Shapes: VSEPR
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2 bonds, 0 lone pairs on Be. Linear.
180.0°
180.0° “2” bonds, 0 lone pairs on C. (treat double bonds as 1 bond) Linear.
OC O
Cl Be Cl
Each C has 2 e-groups. Each H-C-C unit is linear. HC CH
180.0°
180.0°
Predicting Molecular Shapes: VSEPR 2 e-groups:
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3 e-groups:
B has 3 bonds (0 lone pairs). Triangular planar.
Each C has 3 e-groups. Each C is triangular planar.
Cl B Cl
Cl
CC H HH H
120°
Predicting Molecular Shapes: VSEPR
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4 e-groups = tetrahedral e-pair geometry: bond lone pairs pairs 4 0 tetrahedral
.. ..
.. ..
1 bond, 3 lone pairs?
All molecules with only 1 bond are linear!
3 1
triangular pyramidal
2 2
angular
.. ..
Predicting Molecular Shapes: VSEPR
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109.5° 4 bonds, 0 lone pairs. All angles = tetrahedral angle
3 bonds, 1 lone pair. Lone-pair/bond > bond/bond repulsion H-N-H angle is reduced.
.. ..
107.5°
.. ..
.. ..
104.5°
2 bonds, 2 lone pairs. Two lone pairs H-O-H angle even smaller.
H C HH
H
H N HH
O HH
Predicting Molecular Shapes: VSEPR
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VSEPR applies to each atom in a molecule. •! Alkanes: each C is tetrahedral.
Predicting Molecular Shapes: VSEPR
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Tetrahedral O
Lactic acid:
Tetrahedral C
Triangular planar C
Tetrahedral C
H
C C H
H
C
O
O
O
H
H H
..
..
.. ..
.. ..
Tetrahedral O
Predicting Molecular Shapes: VSEPR
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bond lone pairs pairs Shape
5 0 Triangular bipyramidal
Expanded octet atoms:
Remember •! lone pairs
repel the most. •! they get as far
apart as possible.
4 1 Seesaw 3 2 T-shaped 2 3 Linear
6 0 Octahedral 5 1 Square pyramidal 4 2 Square planar 3 3 T-shaped
Predicting Molecular Shapes: VSEPR
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120°
90°
Triangular bipyramidal
..
Seesaw
..
..
T-shaped
..
.. .. ..
Linear
Predicting Molecular Shapes: VSEPR
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.. ..
PF5 SF4 ClF3
F PF F
F F F SF
F
F F Cl F
F
F Xe F
..
..
.. ..
XeF2
..
Predicting Molecular Shapes: VSEPR
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Six e-groups = octahedral e-pair geometry
Octahedral
90°
..
Square pyramid
..
..
Square planar
Equivalent atoms
Predicting Molecular Shapes: VSEPR
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F SF F
F F
F F Br F
F
F F
F Xe F
F
F
SF6
90°
BrF5 XeF4
Predicting Molecular Shapes: VSEPR
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How do atomic orbitals (s, p, d …) produce these shapes?
Orbitals Consistent with Molecular Shapes
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VB theory: bonds occur when atomic orbitals overlap.
H2 – H(1s) overlaps H(1s)
74 pm
HF – H(1s) overlaps F(2p)
109 pm
Orbitals Consistent with Molecular Shapes
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Valence Bond Theory 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, …
•! Why does C form 4 bonds at tetrahedral angles? !! C (1s2 2s2 2p2) !! 2px
1 2py1 Two bonds?
!! p orbitals are at 90° to each other !! Experiments show: tetrahedral CH4, CCl4, …
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One s orbital + one p orbital ! two sp hybrids.
Orbitals Consistent with Molecular Shapes
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sp Hybrid Orbitals Be compounds (BeH2, BeF2 …):
Each sp hybrid (180° apart) holds one e-. Two equivalent covalent bonds form.
2p 2p 2p 2p 2p 2p
2s Isolated Be atom
2s
Promotion Orbital hybridization
Ene
rgy,
E Two unhybridized
p orbitals
Two sp hybrid orbitals on Be in BeF2
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sp2 Hybrid Orbitals B forms three sp2 hybrid orbitals:
!!One s orbital mixes with two p orbitals. !!One p orbital is unmixed.
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sp2 Hybrid Orbitals B compounds (BH3, BF3 …):
Each sp2 hybrid (120° apart) holds one e-. Three equivalent covalent bonds form.
2p 2p 2p 2p 2p 2p
2s Isolated B atom
2s
Promotion Orbital hybridization
Ene
rgy,
E One unhybridized
and vacant p orbital
Three sp2 hybrid orbitals of B in BF3
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sp3 Hybrid Orbitals C forms four sp3 hybrid orbitals:
!!One s orbital mixes with three p orbitals. !!All p orbitals are mixed.
In C, each sp3 hybrid (109.5° apart) holds one e-. Four equivalent covalent bonds form.
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sp3 Hybrid Orbitals N and O compounds (NH3, H2O…) have more e-:
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sp3 Hybrid Orbitals “Octet rule” molecules have tetrahedral e-pair shape. •! sp3 hybridized (CH4, NH3, H2O, H2S, PH3, …)
H
C
H H
H
" bond
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Summary:
Mixed Hybrids (#) Remaining Geometry s+p sp (2) p+p Linear s+p+p sp2 (3) p Triangular planar s+p+p+p sp3 (4) Tetrahedral
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
Hybridization in Expanded Octets
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A carbon atom can have a: •! tetrahedral center (CH4, CHF3 , C2H6…) = sp3 •! triangular-planar center (H2CO, C2H4 …) = sp2
CC H HH H
Hybridization in Molecules with Multiple Bonds
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C (sp2) + C (sp2) overlap (" bond): C C
H
H H
H
Unhybridized C p orbitals each contain one e-.
C C
H H
H " bond
C C
H H
H
overlap
Hybridization in Molecules with Multiple Bonds
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Hybridization in Molecules with Multiple Bonds
Formaldehyde is similar:
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A third type of C center is seen: !! linear center (C2H2, acetylene) = sp hybridized
CC H H
Hybridization in Molecules with Multiple Bonds
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" bond: C (sp) + C (sp) overlap: C C H H
C C H H overlap C C H H
Hybridization in Molecules with Multiple Bonds
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# bonds prevent bond rotation:
Non-rotating double bonds allow cis-trans isomerism to occur.
Hybridization in Molecules with Multiple Bonds
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•!The dipoles cancel because of CO2’s shape. •! the bond dipoles have equal size but point in opposite
directions.
the arrow points to $-, the + shows $+ O = C = O!
$- $- 2$+
Molecular Polarity
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Molecular Polarity
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Molecular Polarity Molecule µ (D) H2 0 HF 1.78 HCl 1.07 HBr 0.79 HI 0.38 H2O 1.85
H2S 0.95 CO2 0 CH4 0 CH3Cl 1.92 CH2Cl2 1.60 CHCl3 1.04 CCl4 0
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•! Polar molecules: bond dipoles do not cancel •! Water is polar:
Observed dipole, µ = 1.85 D!
.. ..
H H O
+
Net dipole
Molecular Polarity
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Molecular Polarity
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Molecular Polarity
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Molecular Polarity
F F
F
C
F
CF4 is non polar
No net dipole
F F
H
C
F
CHF3 is polar
Net dipole
+
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PF5
PF4Cl
PF3Cl2
PF3Cl2
+
+
Molecular Polarity
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Molecules are sticky and attract each other.
Noncovalent Interactions
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London Forces
$+ $- $+ $-
•! 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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Atom Molecule # of e- bp (°C) He 2 &269 Ne 10 &246 Ar 18 &186 Kr 36 &152
More e- = larger attraction = greater stickiness = higher b.p.
F2 18 &188 Cl2 34 &34 Br2 70 +59 I2 106 +184 CH4 10 &161 C2H6 18 &88 C3H8 26 &42 C4H10 34 0
London Forces
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Polar molecules attract each other.
Strength = 5 % 25 kJ/mol.
Dipole-Dipole Attractions
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nonpolar # of e- bp (°C) polar # of e- bp (°C) SiH4 18 &112 PH3 18 &88 GeH4 36 &90 AsH3 36 &62 Br2 70 +59 ICl 70 +97
With equal number of e- (and same shape): dipole/dipole > London
Dipole-Dipole Attractions
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An especially large dipole-dipole attraction. !!10 % 40 kJ/mol !!Occurs when H bonds directly to F, O or N
F, O & N are small with large electronegativities.
!! results in large $+ and $- values.
H-bonds are usually drawn as dotted lines.
Hydrogen Bonds
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H on one molecule interacts with O on another molecule.
Hydrogen Bonds
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Water is a liquid at room T (not a gas).
Hydrogen Bonds
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Phospholipids form lipid bilayers:
Noncovalent Forces in Living Cells
Polar end = hydrophilic (water loving). Nonpolar end = hydrophobic (water hating).
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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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Biomolecules: DNA and Molecular Structure