Organic Chemistry

Structure and Properties of

Organic Molecules

1
 Atomic Orbitals

Electron: wave-like property

~ standing wave
Quantum mechanics: uses math
(wave functions Ψ) to describe the
motion of an electron around a nucleus

1s orbital

Wave function Ψ with positive sign

Sign of Ψ is NOT
electrical charge

Wave function Ψ with negative sign 2

 Atomic Orbitals
2p orbital

Wave function Ψ Probability function Ψ2

y y y (energy density)
y y
z z z
z
z

x x x
x x

2s 2s 2px 2py 2pz

Atomic orbitals can combine/overlap :

• Molecular orbital theory use math to explore atomic orbitals overlap
• Math method : Linear combination of atomic orbitals (LCAO)
• Number of orbitals formed = number of orbitals original
• Orbitals of different atoms interact → molecular orbitals (MO)
• Orbitals of same atom interact → hybrid atomic orbitals 3
 Formation of H2

When 2 H atoms come together, the electrostatic forces change:

• Attraction between electrons and nuclei
• Repulsions between the 2 nuclei
• Repulsion between the 2 electrons

Attractive forces
Max net attraction increase
Most stable state 4
 Formation of H2

Constructive interaction:
2 waves combine and
reinforce each other

𝜎 bonding MO

Destructive interaction:
2 waves combine and
oppose each other

5
𝜎 ∗ antibonding MO
 Formation of H2

LUMO: lowest unoccupied

molecular orbital

HOMO: highest occupied

molecular orbital

In stable compounds, bonding orbitals are filled and antibonding orbitals are empty

6
 Methane and sp3 Hybridization
Carbon atom

4 degenerate
sp3 orbitals

sp3 hybridized C orbital

7
 Ethane
sp3 - sp3 orbitals overlap

sp3 - s orbitals overlap

8
 Double Bonds and sp2 Hybridization

3 degenerated
sp2 orbitals

sp2 hybridized C orbital ethylene

9
 Double Bonds and sp2 Hybridization
𝝅 bond: overlap of two p orbitals perpendicular to the line connecting nuclei

10
 Triple Bonds and sp Hybridization

11

acetylene

sp hybridized C orbital
 In-class Exercise
1.

12

2.
Predicting Molecular Geometry: VSEPR Theory
Presume all e pairs repel each other
→ they will arrange to maximize their distance
→ called valence shell electron pair repulsion (VSEPR) theory

• Depend on number of 𝜎 bond + lone pair (steric number)

• Tetrahedral geometry

CH4 has 4 𝜎 bonds C: sp3

(steric number =4)
13
Predicting Molecular Geometry: VSEPR Theory

• Trigonal pyramidal geometry

NH3 with nitrogen has 3 𝜎

bonds and 1 lone pairs
(steric number = 4)
N: sp3

• Bent Geometry

H2O with oxygen has 2 𝜎

bonds and 2 lone pairs O: sp3
(steric number = 4)

• Trigonal planar
BF3 with B has 3 𝜎 bonds
(steric number = 3) B: sp2
B: sp2 hybrid orbitals

• Linear geometry 180o

BeH2 with Be has 2 𝜎 bonds (steric number = 2)
Be: sp
14
Predicting Molecular Geometry: VSEPR Theory

NUMBER OF
SIGMA BOND

15
 In-class Exercise
3. Use VSEPR theory to predict the geometry of the following

4. Ammonia (NH3) will react with a strong acid (hydronium H3O+) to give an
ammonium ion (acid-base reaction we have just covered). Using VSEPR theory to predict
the change in the bond angles when ammonia is converted to ammonium ion. Explain.

16
5.
 Bond Dipole Moments

Previous class

Dipole moment (𝜇) is an

indication of polarity

17
 Bond Dipole Moments
1.

Example
problem

In-class problem
6.

18
 Molecular Dipole Moments
• Dipole moment of the molecule taken as a whole
• Equal to vector sum of individual bond dipole moments

19
Q.
 Molecular Dipole Moments
• Lone pair: large contribution to molecular dipole moments
• Each lone pair: charge separation (nucleus 𝛿 + and lone pair 𝛿 −)

20
 In-class Exercise

7.

8.

21
 Intermolecular Forces

•Dipole-dipole forces Approach

of two polar molecules with
permanent dipole moments

• The London dispersion forces

Approach of molecules with no dipole moment
Temporarily induced dipole moment by nearby molecules

𝛿− 𝛿+
𝛿− 𝛿+

𝛿− 𝛿+
𝛿− 𝛿+ 22
 Intermolecular Forces

• The London dispersion forces (cont.)

Depends on close surface contact of 2 molecules
Roughly proportional to molecular surface area

Boiling point:
✓ Increase with chain length
✓ Decrease with branch 23
 Intermolecular Forces
• Hydrogen bonding
Not an actual “bond”, just a specific type of dipole-dipole interaction
Happens with any compounds with O−H or N−H bond

H atom bear positive charge (𝛿 +) while N or O bear negative charge (𝛿 −)

✓ Impact on boiling point

Hydrogen bonding strength ~ 20 kJ/mol

Typical single bond (C−H, N − H, O−H) ~ 400 kJ/mol 24
 Chemistry Story

Biomimicry and Gecko Feet

• Ability of gecko to walk upside down, even on very smooth surface
• No chemical adhesive or suction
• Due to intermolecular forces of attraction
between their feet and the surface
• Gecko foot: millions of microscopic
flexible hair, each with smaller hairs

-> extraordinary contact with the surface

Application:

Adhesive bandages in healing surgical wounds

Spiderman gloves and boots

25
In-class exercise
26
 Polarity and Solubility

Intermolecular force affects solubility

Rule: like dissolves like

Solute Polar Non-polar

Solvent
Polar

Non-polar

27
 Polarity and Solubility

Soap

Dissolve oil in water

Dry cleaning

Utilize non polar solvent to dissolve oil

28
 Chemistry Story

Propofol use for anesthesia during surgery (milk of amnesia)

This drug is not soluble in water or blood but dissolve well in soybean oil

Use lecithins (similar to soap) to make propofol and soybean oil soluble in water

29