CONJUGATED MOLECULES

Part 1

What is Conjugation?
For any molecule best structure = lowest energy
•Familiar examples: Which structure is lowest energy?

H
Methane H H
Ethane H H
H
H
H C H H C C C C C
H H
H H
H H H H H H

Square planar or tetrahedral? Staggered or eclipsed?

Lowest energy from minimizing electron repulsion and maximizing p orbital overlap
•Maximum p orbital overlap allows...
Resonance
Conjugation
Aromaticity } What are these?

1
 What is Conjugation?
Case #1: Relative stability of C4H6 isomers
•Isomers: Same molecular formula, different structure.

More stable isomer

4 C (graphite) + 3 H2 (g) DHof = 29.9 kcal mol-1

4 C (graphite) + 3 H2 (g) DHof = 47.7 kcal mol-1

Isomers

•Heat of formation (enthalpy of formation; DHof): Hypothetical enthalpy change when a

substance is synthesized from elements in their standard states.

• Importance: Lower DHof = more stable isomer.

What is Conjugation?
Case #1: Relative stability of C4H6 isomers
H
91.8 H2C C C 1,2-butadiene (an allene)
CH3

No ring strain
Why this order?
Two pi bonds
•Ring strain?
67.7
•Number of pi bonds?
64.6
•Position of pi bonds?
Ring strain
One pi bond
47.7

45.8

Alternating pi-sigma-pi bonds

37.5 H C C CH2CH3
rm

m
H

-1
f)o
E

(D
n
th
p

,k
y
o
fo

a
o

ca

cu

32.0 H3C C C CH3

(c

la
te
f

d)
al

ti

l
ol

al

No ring strain
s-cis-1,3-butadiene
30.7
Two pi bonds
1,3-dienes
29.9 s-trans-1,3-butadiene

0.0 4 C (graphite) + 3 H2 (g)

2
 What is Conjugation?
C=C-C=C C=C-C-C=C
Case #2: Catalytic Hydrogenation of 1,3-Dienes versus 1,4-Dienes

Catalytic hydrogenation: Addition of H2 to a pi bond with a catalyst

H
H H
H2
Example: CH3CH2
C
C
H
CH3CH2 C C H DH = -30 kcal mol-1
Pt
H H
H

Thermodynamics
•Loss: H-H sigma bond, C-C pi bond
Sigma bonds usually stronger than pi bonds
•Gain: 2 x C-H sigma bond
•Conclusion: Catalytic hydrogenation is exothermic (DH < 0)

What is Conjugation?
Case #2: Catalytic hydrogenation of 1,3-dienes versus 1,4-dienes
Catalytic hydrogenation to probe C4H6 isomer stability
•Fact: 1,3-butadiene more stable than 2-butyne (from DHf diagram)

H3C C C CH3 + 2 H2 1,3-butadiene more stable than 2-butyne

+ 2 H2
DH = -65.1 kcal mol-1
DH = -56.5 kcal mol-1

Same molecule = same enthalpy (H)

E
n
th
a
l

•Observation: DH (1,3-butadiene  butane) > DH (2-butyne  butane)

•Conclusion: Less negative DH for catalytic hydrogenation belongs to most stable isomer

3
 What is Conjugation?
Case #2: Catalytic hydrogenation of 1,3-dienes versus 1,4-dienes

The experiment
•Use DH (cat H2) to compare pi-sigma-pi (1,3-diene) versus pi-sigma-sigma-pi (1,4-diene)
1-Pentene (alkene energy benchmark)
H2
DH = -30 kcal mol-1
Pt

1,4-Pentadiene (a 1,4-diene) Predict: DH = 2 x (-30) = -60 kcal mol-1

2 H2
1 3 5
Observe: DH = -60 kcal mol-1
Pt
2 4 Conclusion: No special stability for 1,4-diene

1,3-Butadiene (a 1,3-diene)
2 H2
Predict: DH = -60 kcal mol -1 if stability = 1,4-diene
2 4
Observe: DH = -56.5 kcal mol-1 3.5 kcal mol-1 less than expected
Pt
1 3 Conclusion: 1,3-diene more stable than 1,4-diene

General observation: 1,3-dienes more stable than similar 1,4-dienes

1,3-Butadiene: A Closer Look

What is origin of special 1,3-diene stability?

H H
2.21 Å
H C H C
C H C H

C H K eq > 1 H C
H C C H 2.50 Å

H H
s-cis* s-trans
5% 95%
* s-cis = two pi bonds, separated by sigma bond, in cis arrangement

Major conformation? Torsional strain: s-trans < s-cis

Stability: s-trans > s-cis
Nearly always planar

4
 1,3-Butadiene: A Closer Look
Rotation around the C2-C3 bond
•The s-cis conformation is planar

Indicates movie to play

1,3-Butadiene: A Closer Look

Rotation around the C2-C3 bond
•Perpendicular conformation has lowest torsional strain

5
 1,3-Butadiene: A Closer Look
Rotation around the C2-C3 bond
•The s-trans conformation is planar

http://molview.org/?cid=7845

1,3-Butadiene: A Closer Look

Rotation around the Csp2 - Csp2 bond

Observed
Barrier to rotation: Energy difference between
most stable and least stable conformations.
Pi bonds perpendicular
Predicted

0o 20o 40o 60o 80o 100o 120o 140o 160o 180o

C=C-C=C Dihedral angle

Angle between planes formed by three atoms each.

Conclusion: Energy controlled by more than just torsional strain

6
1,3-Butadiene: Resonance Model

What is the origin of this extra stability, planarity, and barrier to rotation?
•Resonance is often a strong influence on molecular structure, so start there
H H H

H C H C H C
C H C H C H

H C H C H C
C H C H C H

H H H

H C
Resonance hybrid observations
C H •Partial C2-C3 pi bond  explains barrier to rotation
H C •C2-C3 pz orbital overlap  explains planarity
C H

Resonance hybrid

1,3-Butadiene: Resonance Model

The resonance model looks useful, but simplistic. Is it accurate?

•The resonance model predicts...
Model molecules 1,3-Butadiene

C2-C3 bond length (Å)

1.54 1.33 1.48
C2-C3 barrier to rotation
(kcal mol-1)
4.5 ~60 7.5

•Conclusion: Resonance model is / is not accurate despite its simplicity

7
 1,3-Butadiene: Resonance Model
How does resonance explain why a 1,3-diene is more stable than a 1,4-diene?
1,4-diene 1,3-diene

H H H H
e- 
e-  H
H C C H H C C
C C C C C C H

H H H H H H H

•Less resonance contributors •More resonance contributors

•Pi electrons confined between two carbons •Pi electrons roam over four carbons
•Pi electrons have shorter wavelength •Pi electrons have longer
E = hc/ so  wavelength =  energy wavelength

Molecule is less stable Molecule is more stable

CONJUGATED MOLECULES -
PART 2
LECTURE SUPPLEMENT PAGE 38
CH 3

N
H3C CH3

N Mg N
O

H3C
N
O
O

OCH3
H3C
O

H3C CH3

CH 3 CH 3 CH 3

CH3 CH3 CH3

H3C CH3

H3C
H3C CH3 CH3 CH3

CH3 CH3 H 3C CH3

CH 3

8
Part 1 Summary
Adjacent, overlapping p orbitals allows for...
•...more resonance
•...more electron delocalization
Greater stability
•...lower electron energy

Example: more stable than

Consequences of p orbital overlap

•Atoms with p orbitals must be planar
•Partial pi bond(s)
•Barrier to rotation

Extra Stability Limited to 1,3-Dienes?

•1,3-diene has four adjacent p orbitals

•Three adjacent p orbitals is enough to provide extra stability

Example: An amide

Amide resonance contributors: Amide resonance hybrid:

Pi electron delocalization
O O O  provides increased stability


H NH2 H NH2 NH2
H

9
 Extra Stability Limited to 1,3-Dienes?
Another special stabilization example: An amide

O  O


H NH2 H NH2

Resonance hybrid
Nitrogen hybridization?
•Predict: Four attachments = sp3
•sp3 lacks p orbital needed for resonance
•Therefore sp2 to accommodate resonance
•Therefore sp2 to increase stability

I thought hybridization is controlled only by the number of attachments?!

•Energy causes geometry; geometry causes hybridization

Influenced by electron repulsion, resonance, etc.

Extra Stability Limited to 1,3-Dienes?

More adjacent p orbitals = larger electron “playground”

An amide has three adjacent, parallel p orbitals: p orbital overlap gives delocalized pi bonds

p orbital overlap forms pi bonds

Sigma bonds H C
Build your own model
N H
H

Compare with 1,3-butadiene: Four adjacent, parallel p orbitals:

H H H
C C C
H C Build your own model
H H

In general: Adjacent, parallel p orbitals improve molecular stability

10
Conjugation: A Definition
Finally!

Decrease in electron energy

Conjugation: Special stability provided by electron delocalization in three

or more adjacent, parallel, overlapping p orbitals.

Not limited to pi-sigma-pi

(four carbon pz orbitals)

Consequences of Conjugation

Conjugation influences widespread

•Chemical reactivity: Is molecule reactive or inert?

•Molecular structure: Is a molecule (or portion of molecule) flat?

Is bond rotation hindered?

•Physical properties: Color

•Etc.

11
 Consequences of Conjugation
Consequence #1: More extensive conjugation = greater stability
•Influences distribution of products in chemical reaction
•Reaction products:  stability =  amount produced
•Example: Determine major product of this reaction:

O
O O

CH3 - H2O CH3 CH3

H or
CH3
CH3 CH3
HO
HO
H
CH3
CH3 CH3

Ten conjugated p orbitals Six conjugated p orbitals

Which product isomer
More stable Less stable
is more stable?
Produced in greatest amount

Consequences of Conjugation
Consequence #2: Partial pi bond character
•Resistance to conformational change (barrier to rotation)
•Causes planarity of atoms conjugated p orbitals
•Example: Amide linkage between two amino acids in a protein

O O Planar
Barrier to
O 
H rotation
N N
N 
H R R
H R
Less torsional strain More torsional strain
More stable Less stable Resonance hybrid

Barrier to rotation and planarity critical to protein function.

12
 Consequences of Conjugation

Consequence #3: Highly conjugated molecules may be colored

Examples:

Chlorophyll Lycopene b-Carotene

Origin of color: •Some portion of visible (white) light spectrum is absorbed

•Brain perceives remaining light as color

So how does molecular structure control energy of photons absorbed?

Consequences of Conjugation
How does molecular structure control energy of photons absorbed?

Controlled by electron energies

•Molecule absorbs photon (hn)

•Electron is excited to higher energy Lowest Unoccupied

molecular orbital Molecular Orbital
(LUMO)
•Energy of photon absorbed must equal
HOMO/LUMO orbital energy difference (DE) Absorb photon (DE = hn)
DE
E

ro
n
en
g
y
le

er
ct

Highest Occupied
Molecular Orbital
(HOMO)

Ground state Excited state

13
 Consequences of Conjugation
How does molecular structure control energy of photons absorbed?

• number of conjugated p orbitals  DE

•When DE low enough, photons of visible light absorbed
•Unabsorbed portion of visible light spectrum perceived as color

Photon absorbed Observed color

Ultraviolet (UV) Colorless
Violet Yellow
Indigo Orange
Visible light Blue Red
Green Violet
Yellow Indigo
P
ho
to
n

Orange Blue
Red Green

Consequences of Conjugation
How does molecular structure control energy of photons absorbed?

Example Molecules

1,3-Butadiene 1,3,5-Hexatriene Styrene

Four conjugated p orbitals Six conjugated p orbitals Eight conjugated p orbitals
DE = ultraviolet DE = ultraviolet DE = ultraviolet
Perceived color = colorless Perceived color = colorless Perceived color = colorless

14
 Consequences of Conjugation
How does molecular structure control energy of photons absorbed?

Example Molecules

OH O

Retinol (vitamin A) Retinal

Ten conjugated p orbitals Twelve conjugated p orbitals
Photons of hn = DE are violet Photons of hn = DE are indigo
Perceived color = yellow Perceived color = orange

Consequences of Conjugation
How does molecular structure control energy of photons absorbed?

Example Molecules
H3C CH3

Not conjugated
CH3 CH3 CH3

CH3 CH3 CH3

Not conjugated
Lycopene
H3C CH3
22 conjugated p orbitals
Photons of hn = DE are blue
Perceived color = red

15
NEWS 15 AUGUST 2019

Chemists make first-ever ring of pure carbon

Elusive 18-atom ‘cyclocarbon’ could be a step towards molecule-scale transistors.

https://www.nature.com/articles/d41586-019-02473-z

INTRODUCTION TO
AROMATICITY
LECTURE SUPPLEMENT PAGE 46

H C H
C C

C C
H C H

16
 Historical Background
London, 1825
•Street lamps fueled by gas derived from whale and cod oils
•Liquid benzene (structure unknown) condensed in pipes
•Analyzed by Michael Faraday
•Vapor density experiment reveals MW = 78; formula = C6H6
•C:H ratio 1:1 implies high reactivity like acetylene (HCCH)
•However benzene is fairly inert:
Stable at room temperature
More resistant to catalytic hydrogenation (H2/Pt) than related substances

Conclusion: Benzene is not like related substances

Benzene Structure?

328 C6H6 isomers possible

•Problem remained unsolved for 40 years, until two key ideas formulated:

1857: Fredrich Kekulé suggests carbon can form four bonds

1864: Alexander Crum Brown suggests carbon can form multiple bonds

C C

C C

17
Break

The C6H4Cl2 Isomer Problem

Structure must be consistent with experimental facts
Cl2
Fact: C6H6 C6H4Cl2 Three isomers

Some benzene structure candidates:

H
X H
X X
Dewar benzene Prismane Fulvene
Six C6H4Cl2 isomers Four C6H4Cl2 isomers Nine C6H4Cl2 isomers

2,4-Hexadiyne
H3C C C
X C C CH3
Two C6H4Cl2 isomers

None of these are the correct structure for benzene

18
 Benzene Structure?
Kekulé’s Dream

1866: Solution to the benzene problem comes to Kekulé in a dream.

“During my stay in Ghent [Belgium] I resided in elegant bachelor quarters in the main
thoroughfare. My study, however, faced a narrow side alley and no daylight penetrated
it. For a chemist who spends his day in the laboratory this mattered little.”

“I was sitting writing at my textbook but the work did not progress; my thoughts were
elsewhere. I turned my chair to the fire and dozed. Again the atoms were gamboling
before my eyes. This time the smaller groups kept modestly in the background. My
mental eye, rendered more acute by repeated visions of the kind, could now
distinguish larger structures of manifold conformation: long rows, sometimes more
closely fitted together all twining and twisting in snakelike motion.”

Benzene Structure?
Kekulé’s Dream

“But look! What was that? One of the snakes had seized hold of its own tail, and the
form whirled mockingly before my eyes. As if by a flash of lightning I awoke; and this
time I also spent the rest of the night in working out the consequences of the
hypothesis.”
H

H C H
C C

C C
H C H

The Ouroboros Kekulé benzene

19
Problems with Kekulé Benzene Structure
The Isomer Problem
•Bond length: C-C > C=C
•Therefore Kekulé structure suggests two isomers for 1,2-dichlorobenzene:

H H

H H Cl
Cl

Shorter C-C bond Longer C-C bond

H Cl H
Cl
H H

Observation: These 1,2-dichlorobenzene isomers never isolated or detected

Conclusion: Kekulé structure cannot be accurate

Problems with Kekulé Benzene Structure

Kekulé’s solution to the isomer problem

•Isomers in very fast equilibrium
H H

H
Cl H Cl Cl
Cl
Cl
very fast

Cl Cl
Cl
H H
Cl Cl

H H

•Separate structures cannot be isolated or detected

•Test: Regardless of equilibrium rate, C=C present
 Expect typical C=C reactions

20
Problems with Kekulé Benzene Structure

Test benzene in typical alkene reaction

Br
Br2 Addition reaction: Product
Alkene reaction: has all atoms of reactant plus
Br new groups

Both have pi bonds

Prediction for Kekulé benzene:
Similar functional groups = similar reactions
Br
Br2

Br

Problems with Kekulé Benzene Structure

But in fact...

Br

X
Br2
No reaction occurs
Br

H Br
Br2

FeBr3

•Catalyst required: Benzene less reactive than alkene

•Substitution (not addition) occurs
•Substitution reaction: Portion of reactant is replaced

21
 Revised Kekulé Benzene Structure

How to revise Kekulé structure to be consistent with the actual properties?

•Very rapid equilibrium reminiscent of resonance

•Kekulé benzene “isomers” = resonance contributors

•These "isomers” have no discrete existence
•Benzene is not “just three alkenes in a ring”
•Resonance hybrid:

Prediction: All C-C bond lengths equal

or
•Verified by x-ray diffraction (Kathleen Lonsdale; 1928)

Revised Kekulé Benzene Structure

What is so special about Kekulé benzene?

•How can we explain its special stability?
Resonance?
Conjugation?
•How do we measure this special stability?
Catalytic hydrogenation

22
 Measuring the Special Stability of Benzene
Compare cyclohexene and benzene via catalytic hydrogenation

H2
DH = -28.6 kcal mol-1
Pt

3 H2
Prediction: If benzene is “just three alkenes”...
DH = 3 x (cyclohexene + H2) = 3 x -28.6 = -85.8 kcal mol-1
Pt
(~10 kcal mol-1 less if conjugation is included)

Observations
•Benzene +3 H2 requires more heat and more pressure than cyclohexene + H2
• DH (benzene + 3 H2) = - 49.8 kcal mol-1
Conclusions
• DH (benzene + 3 H2) < DH [3 x (cyclohexene + H2)], so benzene more stable
•Extra stability = 85.8 - 49.8 = 36.0 kcal mol-1
= Resonance energy
= Aromaticity

Why Called “Aromatic”?

Why is this special stability called “aromaticity”?
•First molecules known to contain benzene ring have pleasant aromas; hence “aromatic”
•But not all benzene-containing molecules have pleasant odors
OH
O OCH3 O OH
CH3
OCH3 SH

OH

H O

Toluene Methyl salicylate Vanillin Benzoic acid Thiophenol

glue oil of wintergreen vanilla flavor odorless skunky

23
Is Benzene Ring the Only Aromatic Structure?

Observation: Aromatic stability due to resonance of C=C in ring

Conclusion: Other rings with resonance might also be aromatic

Examine other cyclic CnHn isomers with alternating pi bonds

Cyclobutadiene C4H4
•Many synthesis attempts fail
•1965: Isolated in frozen argon matrix at 4 K Cyclobutadiene is very reactive
•Unstable...not aromatic?
•Instability due to ring strain?
•Quantum mechanics: Instability due to two unpaired electrons

Conclusion: No special stability; not aromatic

Is Benzene Ring the Only Aromatic Structure?

Cyclooctatetraene C8H8 •Synthesis: 1911, Richard Willstätter

Hydrogenation: Reacts easily with H2/Pt:

4 H2
Shape = tub
Pt

Conclusion: No special stability; not aromatic

24
Is Benzene Ring the Only Aromatic Structure?
Benzene is not the only aromatic molecule
Aromatic:

Benzene Naphthalene Pyridine Furan Cyclopentadienyl

anion

Not aromatic: Not all cyclic CnHn molecules are aromatic

Cyclobutadiene Cyclooctatetraene 1,3-Cyclohexadiene Cyclopentadienyl

cation

•How to predict aromaticity? What are the molecular structure requirements?

How to Predict Aromaticity?

Studies on many molecules reveal three requirements for aromaticity

Required: Closed loop of p orbitals (loop of sp2 or sp atoms)

Required: Atoms of closed loop must be planar (p orbital overlap)

To override planarity (and aromaticity) strain must be severe.

36 kcal mol-1 in benzene

Required: Closed loop must contain 2, 6, 10, 14... pi electrons (Hückel’s Rule)
•Series described by 4n+2 = pi electrons (n = integer: 0, 1, 2...)
•Six pi electrons is most common number (benzene)

2 + 2 + 2 = 6 pi electrons (4n+2 = 6; n = 1)

25
How to Predict Aromaticity?
How much strain is too much?

Aromatic Aromatic Aromatic Not aromatic

Stabilization from aromaticity Destabilization from strain

Aromaticity: A Definition

Aromaticity: Special stability possessed by a molecule which has 4n+2 (n = an

integer) pi electrons contained within a closed loop of adjacent, parallel,
overlapping p orbitals.

26
How to Predict Aromaticity?
Additional examples

Naphthalene
Closed p orbital loop? 

Planar? No significant reason to be nonplanar 

Pi electron count? 5 C=C @ 2 e- each = 10

(4n+2 = 10 when n = 2)


Conclusion: Naphthalene is / is not aromatic

How to Predict Aromaticity?

Additional examples
Oxygen Oxygen
sp3 sp2
Furan
Closed p orbital loop? 
O

sp3; no p orbital
sp2; one lone pair in p
one lone pair in sp2

Planar? No significant reason to be nonplanar 

Pi electron count? 2 C=C @ 2 e- each = 4

1 lone pair in oxygen p = 2
Total = 6 

Conclusion: Furan is / is not aromatic Build a model!

27
 How to Predict Aromaticity?
Additional examples and requirements

•Closed loop p orbitals do not have to be occupied

Example: Tropylium cation

Unoccupied p orbital
Is tropylium cation aromatic?

•Atoms must all lie in closed loop for their pi electrons to participate in aromaticity
Example: Cyclopentadienone

O Oxygen not in closed loop

These pi electrons do not add to aromaticity

Is cyclopentadienone aromatic?

Consequences of Aromaticity
•Aromatic rings are planar
•Aromatic rings are more stable than similar nonaromatic structures

Biological example: DNA nucleobases are aromatic

NH2 O

N H
N N

N O N N NH2

O NH2

H3C H
N N
N

N O N
N

•Planarity: More bases (more genetic information) into smaller space

•Chemical stability: Not easily degraded; effectively preserves DNA function
•Pi stacking: A noncovalent interaction; adds stability to the molecule

28
End for today

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