Chem 125 Lecture 18
10/15/08
This material is for the exclusive use of
Chem 125 students at Yale and may not
be copied or distributed further.
It is not readily understood without
reference to notes from the lecture.
Four Functional Groups:
Carbonyl 
Amide
Carboxylic Acid
Alkyl Lithium
(then we’ll have a complete change of perspective)
Resonance:
Intramolecular
HOMO/LUMO Mixing
••
N
C
O
Why the Amide Functional Group
is not an Amine and a Ketone
Carbonyl
Amine
LUMO
vs.
Amide
O
C
O
net
O
C
HOMO
N
C
N
Naïve Prediction
Stable
N
Experimental Observation
More Stable by 16 kcal/mole (1/4 C-N)
Resonance as a
Long N-C
Shorter N-C
Make
&
Break
correction
to
Crucial
for
Short C=O
Longer C=O
Structural

*
“LUMO”
a
naïve,
localized
initial
Pyramidal N
Planardrawing
N
Biology
…
by 0.14Å
…
by 0.03Å
C=O
!
(best overlap)
N
Easy N-C Rotation
Barrier to Rotation 16 kcal/mole
wrecks
*C=O
-nN overlapSkin works
O
C
N

*
Basic and
Acidic
Relatively
Unreactive
nN “HOMO”
C=O
might as well rehybridize
PartialDipoles
C=N
(mostly) Opposing
Partial C-O Strongly Dipolar ~1/3 e- transfer
nNH
Double Bond
3
Single Bond
(in  direction)
NO
HOMO : formamide
 electron pair
“from” N
shared with C=O
creates
electric dipole
Repeating Unit in Protein -Helix
+
-
(reducing backbone “floppiness” by 1/3)
=
Stabilized by electrostatic “Hydrogen Bonding”
and by local planarity of C-N-C-C groups
Acidity of Carboxylic Acids
R-OH
R-C
R-C
pKa ~16
O
OH
O
pKa ~5
R-C
O
O
+ H+
1011  stronger! (Less “Uphill”)
+
OH
R-O + H+
HOMO/LUMO stabilizes
neutral acid compared to ROH.
Predicts more uphill?
R-C
O
O
higher
HOMO/LUMO REALLY
stabilizes carboxylate anion.
HOMO ()
Aggregation
of CH3Li
LUMO+1
LUMO
()()
2HOMO ()
LUMO+1 ()
Dimerization
2LUMO+1 ()
Aggregation
of CH3Li
HOMO ()
Rotate to
superimpose
the red lobes.
3-Center
2-Electron
Bonds
use 2 AOs
of each Li
Aggregation
of CH3Li
LUMO+1 ()
LUMO ()
Dimerization
Two vacant
Li+ AOs
stabilize
unshared
pair of C
HOMO ()
LUMO+1 ()
LUMO+1 ()
HOMO ()
LUMO+1 ()
Aggregation
of CH3Li
rotated 90°
Excess Ether Rips
Aggregates Apart by
bonding with Li
AOs.
NON-BONDED INTERACTIONS
Last Valence
& SOLVENT
EFFECTS ARE
AO of
Li OF LORE.
A VITAL
PART
(vacant) ionization)
(e.g. facilitating
H3C
:
O
CH3
Distorted
Cubic
Tetramer
LUMO
(1 of 4)
3 vacant
Li+ AOs
stabilize
unshared
4-Center
2-Electron pair of C.
Bond HOMO
(1 of 4)
Aggregation
of (CH3Li)4 • 4 CH3OCH3
We have seen amazing modern tools for
revealing the Å / psec world of molecules:
SPM
X-ray Diffraction
Spectroscopy: IR, ESR, (NMR, etc.)
Quantum Mechanics
(computer "experiments")
But organic chemists
were not at all surprised
by what they showed!
How Did
They Know?
17th Century
Hooke (1665)
Luther
Reformation
Bacon
Instauration
Columbus Copernicus
Navigation Revolution
1500
Newton
Gravitation
Lavoisier
Oxidation
Planck
Quantization
Us
1600
1700
1800
1900
2000
Science & Force Laws Development of Electron bonds:
the Organic
observation
Structural Model
&
Robt. Hooke
quantum
(1635-1703)
mechanics
Yale Chemistry 1901S
Cf.
Clairvoyant
Benzene


Greek symbols denote
substituent positions.
Sheffield Chemistry Lab (SSS)
(only quantitative tool)
Yale Chemistry 1901S
Quantitative Tools?
Burettes
Balance
C. Mahlon Kline
(1901S)
Analytical Balances Were Not Portable
Kline
Biology
Tower
(1965)
Kline
Chemistry
Laboratory
(1964)
Quartz
Silliman Crystal
Silliman Crystal
Boyle Lavoisier
Berzelius etc.
Wöhler/Liebig
Genealogy
GenealogyBottom
Genealogy Top
End of Lecture 18
Oct. 15, 2008