Transcript Chem 125 Lecture 10 9/26/07 Preliminary

Chemistry 125: Lecture 17
October 12, 2009
Carbonyl, Amide, Carboxylic
Acid, and Alkyl Lithium
The first “half” of the semester ends by analyzing four functional groups in terms of the interaction of
localized atomic or pairwise orbitals. Analyzing *C=O predicts a trajectory for attack by a high HOMO.
Bürgi and Dunitz compared numerous crystal structures determined by X-ray diffraction in order to
validate this prediction. Key properties of biological polypeptides derive from the mixing of localized
orbitals that we associate with “resonance” of the amide group. The acidity of carboxylic acids and the
aggregation of methyl lithium into solvated tetramers can be understood in analogous terms. More
amazing than the power of modern experimental and theoretical tools is that their results did not surprise
traditional organic chemists, who already had developed an understanding of organic structure with much
cruder tools. The next quarter of the semester is aimed at understanding how our scientific predecessors
developed the structural model and nomenclature of organic chemistry that we still use.
(to be supplemented with after-class Spartan session)
For copyright
notice see final
page of this file
Shape of "Frontier" Orbitals
H
LUMO
O C H
HOMO
(6 valence pairs)
Plum
3dxz
Pudding
MOs
3dxy
ABN
2pz
AON
3s
2py
45% 2pO :
55% 2pC
Low LUMO
Pairwise Mixing
Analysis
2pC)
Poor overlap () ; Poor E-match (2pO <
2px
2s
C-O
0.003
0.3
0.1
0.03
0.01
e/ao3
 Bonding
55% 2pO : 45% 2pC ?
van der Waals radii
(1.5Å) O
holds its electrons
more closely than C (1.7Å)
Nodes through nucleimostly
(AON),a p-rich hybrid atomic orbital
not between atoms of
(ABN)
Oxygen
Lower of Oxygen’s
“Unshared" Pairs
some O-C bonding
some C-H bonding
with backside of C hybrid
until 1980s
From what direction
should a nucleophile
HOMO approach
the * LUMO
of the C=O group?
Also
Bürgi-Dunitz
Angle
Nu
H2C O
is
better
than
Nu
H 2C O
(where Nu means “nucleophile”)
furthest
from nodes
Bürgi-Dunitz
Angle
From what direction
should a nucleophile
HOMO approach
the * LUMO
of the C=O group?
N
N
R
C
O
from H. B. Bürgi, J. D. Dunitz
Accts. Chem. Res. 16, 153 (1983)
N.B.
Structure Superposition
from 14 Crystals (A-O)
Containing N: and C=O
R
Bürgi-Dunitz
There is another R group
Angle
directly behind
this one.
(110°)
C
O
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 mixing 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
only 2 AOs
of each Li
Aggregation
of CH3Li
LUMO+1 ()
LUMO ()
Dimerization
Vacant
Li+ AOs
stabilize
unshared
pairs of CH3
HOMO ()
LUMO+1 ()
LUMO+1 ()
HOMO ()
LUMO+1 ()
Aggregation
of CH3Li
rotated 90°
Excess Ether Rips
Aggregates Apart by
bonding with Li
AOs to form
CH3Li • 3 O(CH3)2
NON-BONDED INTERACTIONS
Last Valence
& SOLVENT
EFFECTS ARE
AO of each
A VITAL
PARTLiOF LORE.
(vacant) ionization)
(e.g. facilitating
H3C
:
O
CH3
Distorted
Cubic
Tetramer
(CH3)2O
CH3OCH3
LUMO
(1 of 4)
3 vacant
Li+ AOs
stabilize
unshared
4-Center
2-Electron
O(CH3)2 pair of C.
Bond HOMO
(1 of 4)
Aggregation
of (CH3Li)4 • 4 CH3OCH3
Spartan
Demonstration
you choose
the functional group
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
1600
Newton
Gravitation
1700
Hooke
Lavoisier
Oxidation
1800
Coulomb
Science & Force Laws
Planck
Quantization
Us
1900
2000
Schrödinger
The Organic
Electron Bonds:
Structural Model
Observation
&
&
Chemistry
Quantum
Mechanics
End of Lecture 17
Oct. 12, 2009
Continue for Optional Spartan Demo
Copyright © J. M. McBride 2009. Some rights reserved. Except for cited third-party materials, and those used by visiting
speakers, all content is licensed under a Creative Commons License (Attribution-NonCommercial-ShareAlike 3.0).
Use of this content constitutes your acceptance of the noted license and the terms and conditions of use.
Materials from Wikimedia Commons are denoted by the symbol
.
Third party materials may be subject to additional intellectual property notices, information, or restrictions.
The following attribution may be used when reusing material that is not identified as third-party content:
J. M. McBride, Chem 125. License: Creative Commons BY-NC-SA 3.0
Enol by Spartan
The narrative for this timed ppt comes after the
normal lecture on the same WMA file, following
some after class questions. It begins at 57’36”.
Click the forward arrow at 58’10”, after JMM says
“So we want an enol. So we want to build a mol…
we want to select that set of nuclei.”
Sometimes the timing malfunctions a bit, which
you can get around by pressing the arrow keys, if you
wish.
0.03
0.003
0.3
End