I, too, started small..

Peter Vollhardt
University of California at Berkeley
Organic Chemistry:
The Chemistry of Carbon
Organic
Chemicals
in
Action
Chemicals
Saccharin (1879): 300 Times
as Sweet as Sugar
Mmmmmmmmmmmmmhhhh!!!!
Chemical Warfare in Nature:
Benzoquinone,
Hydrogen
peroxide,
100C
The Bombardier Beetle
Seahare
PinkFloyd
Chemical Protection in Nature
Nature is not always green.
Polyacetylene:
Organic Conductors
The Polyamide
Kevlar
Bulletproof!
Organics Harder Than Metal
Polystyrene
from styrene
Suntan lotion
The Sands Hotel, Las Vegas,
11.26.1996
Nature is the Biggest Polluter
Top Four US Prescription Drugs
Total U.S. sales of pharmaceuticals reached $224 billion in 2003, with
lipitor leading at $6.3 billion.
Male Chromosomes
Clones
DNA: the Double Helix
Ban Dihydrogen Monoxide
Matthew
James
Tvedten
(Poison:
Chlordane)
Michigan
(1/27/81)
6,000+and
continuing at a
rate of 10 to
15 per month
(Poison: methy
l isocyanate
and others)
Bophal, India
(Deaths since
12/2/84)
Death/Injury
ongoing (Poison:
Dow's Agent
Orange) New
Plymouth, NZ
(1965-present)
Jesse
(Poisons:
NIX
and
Lindane)
U.S.
(9/11/93)
Dedicated to the Martyrs of Pesticide Poisoning
May they (and we) find justice
Baby Evans
(Poison:
Termiticide) St.
Petersburg, FL
(5/2000)
Colette
Chuda
(Poison:
various
pesticides)
New
Jersey
(4/21/91)
Cindy
Duehring
(Poison:
various
pesticides)
Bismark, ND
(6/30/99)
24 Children
(Poison: methyl
parathion by
Bayer)
Tauccamarca,
Peru (10/24/99)
Julia
Kendall
(Poison:
Malathion)
California
(7/12/97)
Marianna Cates
and Family
(Poison: various
agricultural)
Ulster County,
New York
(6/1995)
Memorial
547 Men, Women and Children will Die today
from Pesticide Poisoning
(Statistically known as "acceptable risks" for pesticide poison registration)
No Chemicals in Kailua
Water: The Solvent of Life
The Hydronium Ion
Orbital
H
H
H
O
Charge
Cornflowers: Blue
(Unprotonated)
Poppies: Red (Protonated)
What to Expect: an Outline
C C
H
H
H
H
H
H
Structure and Bonding
Alkanes
Haloalkanes
Cycloalkanes
Stereoisomerism
CH3 Cl
- +
CH2
CH2
CH2
H2C
H2C
CH2
Basic Reactions
CH
3
H + Cl
2
CH
3
Cl + HCl
hv,
Substitution
CH
3
Cl
+
K I
+ -
CH
3
I K Cl
+ -
+
Radical Halogenation
Reaction versus Mechanism
CH
2
CH
2
+ H
2
C CH
2
H I
base
Elimination
Reaction: The recipe and molecular alteration.
Mechanism: What is the exact pathway by which
alteration occurs?

Functional Groups
OH C
C C
C C
RCOH
O
R
R
O
C
NH
2
R
Spectroscopy: NMR, IR
Synthesis:
Whler (1828):
Made an organic compound
from an inorganic salt.
Pb(OCN)
2
+ 2 H
2
O + 2 NH
3
2 H
2
NCNH
2
+ Pb(OH)
2
O
Urea
How do we make penicillin?
O
O
N
N
S
COOH
Or cubane ?
H
H
H
H
H
H
H
H
Before we get into this, we need to review the basics.
H
Bonding
Atom 1 + Atom 2 A:A or A A
favorable
Rules:
1. Opposite charges attract each other
(Coulombs Law).

2. Electrons spread out in space
(delocalization).
3. Noble gas configuration is desirable.
1736-1806
Covalent Bonding: Sharing
Electrons
Dimensions:
Nuclear diameter ~ 10
-15
m
Electronic orbit ~ 10
-10
m

five
orders of
magnitude
Mass ratio proton : electron = ~ 1800
Internuclear Potential
Ionic Bonding:
No Sharing of Electrons
Who donates and who accepts?
Valence electrons
Duet
Octets
Partial Periodic Table
Why Do Elements React?
Aim
1. Ionic Bonds
Li
2,1
Na
2,8,1
F
2,7
[Li
2
]
+
[Na
2,8
]
+
[F
2,8
]
-
+1e
-1e
-1e
Therefore:
+
-
Noble Gas Configuration
2 Na F F
2
2 Na +
Transfer
of
Valence
Electrons
Cov
ale
nt
Bon
ds
-4e
Shows only
valence e
(He)
(Ne)
Compromise: electron-sharing
C
. .
H
H
H
H
. .
.

.
.

.

H O H
.

.
.

.

. .
. .
2. Covalent Bonds
C
4+
+4e
4 H

C

C

2 H
2
O
2
+

+

C
4-
Elements in the middle of the periodic table
have a problem with electron affinity (EA)
and ionization potential (IP):
Lakehurst, NJ,
May 3, 1937
The Hindenburg:
3. Most Bonds Are Between Covalent and
Ionic:
Polar Covalent
Pauling electronegativity scale
H
I Cl

H
3
C
F

:

:

: :
-
+
:

:

: :
-
+
- +
F

:

:

: :
A
:
B

- +
1901-1994 Nobel prizes for chemistry and peace
push pull
:
0.3 < 0.3 2.0 < 2.0
Covalent Polar
Covalent
Ionic
Increase
Decrease
The Shape of Molecules
Controlled by valence electron repulsion
Diatomics: linear (of course), e.g.
Triatomics: either linear (i.e. not bent), e.g.
H
:
H Li
:
H
F

:

:

: :
F

:

:

: :
Be F

:

:

: :
F

Be
or bent, when there are lone e-pairs, e.g.
Tetraatomics: either trigonal, e.g.
O

H
H
Cl
:

:

: :
Cl
Cl
B
not
F

:

:

: :
F

:

:

:
Or pyramidal, when there are lone e-pairs, e.g.
Pentaatomics: tetrahedral, e.g.
But other shapes are possible, when there are more
electrons,
e.g. in transition metals (octahedral etc.).
H
H
H
H
N
:

H
H
H
C
Lewis Structures
Draw molecular skeleton (given) Rule 1:
Count total number of valence electrons Rule 2:
Octet (Duet) Rule
Provide octets (duets for H) around all atoms
Rule 3:
How to distribute valence electrons:
CO
2
O C O CH
4
C
H
H H
H
C
.
.
.
.
. .
O
:
.
.
H Br
:

:

:
.
.
H
:
H
F

:

:

: :
F

:

:

:
H
H
Take care of charges, if any. Charges occur
when the formal effective electron count
around the nucleus differs from valence
electron count.
Effective electron count: Each bond with two
shared electrons counts as 1e; lone pairs count as 2e.
H
3
O NO
CO
Rule 4:
:
N
: : :
O
:
+
:
C
: : :
O
:
+ -
H : O : H
H
.
. .
.
+
Valence electron count: Rule 2 (# of valence electrons).
+ +
Example:
1. Atom arrangement:
2. Valence electrons:
3. Octet rule
Shortcut:
1. Connect all bonded atoms with 2e line.
2. If there are e left, add them as lone pairs to any
atom to give it an octet until no e left.
3. If some atoms lack octet, move lone pairs into
shared positions.
CO2
:
..
..
..
:
..
O C O
O C O
..
..
..
..
O C O
:
..
..
..
:
..
O C O
O C O
O 6e, C 4e 16e total
Gilbert Lewis
(arrived in Berkeley in 1912)
Resonance
Often several octet structures are
possible for a molecule: Resonance forms
Form A form B
move
electrons
(pairs)
Molecule is a
superposition of
these forms
Carbonate, CO
3
2-
. All forms are equivalent
O
O
C
O
- -
O
C
O
-
O
C
O
-
-
:
O
:
..
-
:
O
:
..
The carbonate ion is delocalized:
symmetrical!
Electrostatic Potential Map: Red = relatively electron rich
Blue = relatively electron poor
Resonance Forms
O
C
O
-
-
:
O
:
..
Rules
1. Octet rule (wins over all other)
Nonequivalent Resonance Forms
6e
-
major
O O
H
C C
H H H
+
6e
major
N N O
+ +
which ones are better?
O
2. When there are two or more forms with
complete octets: electronegativity rules.
Example: enolate ion
charge on more
e-negative element
major
H
-
-
H
H H H
H
C C C C
O O
But:
6e
major
N N O
+ +
O
When in doubt, rule 1 wins !
3. Minimum charge separation
Formic acid
major
-
H
C
C
H
H
H
O
O
+
O
O
Note: Rule 1 wins ! :
C
: : :
O
:
+
-
1900 Planck, Einstein: Light = photons E = h
= c/ c = 300,000 km sec
-1
Atoms absorb/emit energy in discrete packages:
quanta (to avoid ultraviolet catastrophe)
1923 DeBroglie: All mass (m) moving with velocity v has a
wavelength .
Quantum Mechanics
Light and objects as waves or particles
h
mv
=
1927 Heisenberg: Uncertainty () principle
(position) x (momentum) > h
h = Plancks constant = 1.34 x 10
-34
cal sec
Orbitals: Solutions to wave equations
(wavefunctions)
Born: Square of a value of the
wavefunction = probability of finding
the electron there
1927 Schrdinger: Wave equations for
an electron moving around the
nucleus
Spherical (three-dimensional) shape.
Contrast to mechanical waves
(guitar string, rubber band)
Two-
dimensional
wave
+/- = signs, not charges
Orbitals
node
amplitude
+
-
0
ball
spherical
eight
Actual solutions: 1s, 2s, 2p
x
, 2p
y
, 2p
z
,
3s, 3p
x
, 3p
y
, 3p
z
, etc.
(increasing energy)
+
-
node
Most important orbitals (for us):
#s are related to
classical shells
s Orbital p Orbital
The 1s Orbital
s-Orbital
The 2s Orbital
The Three 3p Orbitals
p-Orbital
Energy diagram depicting solutions as energy levels:
There are rules
for filling up
levels with e
1. Lower energy orbitals filled first (closed shell)
2. Pauli: Exclusion principle: 2e max
3. Hunds rule: Equal energy orbital (i.e. p
x,y,z
) filled
with one e each first
electrons (He)
1s
2s
p
x
p
y
p
z
Aufbau Principle
or: where the electrons go
Energies of Orbitals Calculated for H Atom
Therefore,
electronic
configurations:
H(1s)
1
; He(1s)
2
;
Li(1s)
2
(2s)
1
;
Be(1s)
2
(2s)
2
;
B(1s)
2
(2s)
2
(2p)
1
;
C(1s)
2
(2s)
2
(2p)
2
.
Bonding occurs by overlap of atomic
orbitals to give molecular orbitals
In phase overlap bonding molecular orbital
Out of phase overlap antibonding molecular orb.
antibonding
(node)
bonding
Energy
diagrams
1s 1s
1s
2p
Bonding
E
-Orbitals split energy levels when entering
into overlap.
-The better the overlap [e.g. same type of
orbital, same energy (shell)], the larger the
splitting.
-For orbitals of unequal energy, the higher
orbital goes up, the lower down.
e go down
no e
good
bad
1s
2p
The Types of Orbital Overlap
This is Real!
Direct Observation of d-Orbitals in Cu
2
O
Zuo et al. Nature 1999, 401, 49.
Li : H 2s + 1s no shape issues
H : Be : H is linear; but Be atom
has filled shells (1s)
2
(2s)
2
!
How does it bond? Use an empty p orbital:

Hybridization and Shape
-
++
-
This allows for bonds, but gives
wrong structure:
Intraatomic overlap of 2s and one 2p
orbitals generates two new hybrid
molecular orbitals: s + p two sp hybrids,
with linear arrangement:

Better: Hybridization of Orbitals
sp-Hybrid
Note: n atomic orbitals n new orbitals
We shall see next that other
combinations of intraatomic overlap
(hybridization) are possible:
s + p + p 3 sp
2
with trigonal shape
s + p + p + p 4 sp
3
with tetrahedral
shape

Example: Bonding in BH
3
.
Hybridization to Trigonal
sp
2
-Hybrid
Bonding in Methane:
Hybridization to Tetrahedral
sp
3
-Hybrid
Methane
Bonding in Ethane:
Overlap of Two sp
3
Hybrid Orbitals
Ethane
More sp
3
Hybrids: NH
3
and H
2
O
Double and Triple Bonds:
A Preview
Ethene Ethyne
Delocalized Electrons:
Fe Atoms on a Cu Surface
Molecular Models:
Use Them!!!
The Dashed-Wedged Line
Notation
Rhonda Walba