3 Determination of Mechanism

Philosophy of mechanistic studies:

No reaction could be determined with 100% certainty.
One can only disproof a hypothetical mechanism, not
proof.
As the result, an approved, last mechanism is said to be
reasonable, not correct.
More than one method would be needed to confirm, and
their results must all be consistent.
Gather information from many experiments until enough
to induce or extrapolate to a general conclusion.
Occams razor: In the event that several hypotheses are
found to fit the facts, the simplest one is given preference.
1

3. Determination of Mechanism
3.1 Identification of products
3.2 Determination of the
presence of intermediates
3.2.1 Isolation of intermediates
3.2.2 Detection of intermediates
3.2.3 Trapping of intermediates
3.2.4 Addition of a suspected
intermediate

3.3 Study of catalysis

3.3.1 General acid catalysis
3.3.2 Specific acid catalysis

3.4 Labeling study

3.4.1 Group labeling
3.4.2 Isotope labeling
3.4.3 Crossover experiments

3.5 Isomeric selectivity study

3.5.1 Regiochemical evidences
3.5.2 Stereochemical evidences

3.6 Kinetic studies

3.6.1 Measurement of rate
3.6.2 Mechanistic information
obtained from kinetic
studies
3.6.3 Rate law

3.7 Kinetic isotope effects

3.7.1 Deuterium isotope effects
3.7.2 Primary isotope effects
3.7.3 Secondary isotope effects
3.7.4 Solvent isotope effects

3.1

3. Determination of
Identification ofMechanism
products

Mechanism must be compatible with its products including

the by-product.
e.g. von Richter Rearrangement
COO - At the first glance, the

NO 2

mechanism was though as a

simple nucleophilic substitution
of NO2 by CN- followed by the
hydrolysis of CN- to CO2H

CNNO 2

COOCN-

However,
Br

Br

Early proposed
mechanism
Br

Br

Br

CN-

H
NH

CN
O

Br

Br

Br

H2O
COOH

N O

H2O

-NO2, -NH3

NH
O

-H+

NH
O

N O

But, from its product study, none of the NO2 or NH3 gas
was found, instead, the N2 gas was detected.

The mechanism was then fixed as follow:

Br

Br

Br

CN-

H
NH

CN
O

Br

Br

Br

H2 O

H 2O

-NO2 , -NH 3

COOH

NH
O

-H +

NH
O

N O

Br

Br

Br

-H 2O

H 2O
-N 2
COOH

N O

O
N N

NH 2

3.2 Determination of the

presence of intermediates

3.2.1 Isolation of intermediates

Isolate the intermediate which can give the same products when
subjected to the same reaction conditions at a rate no slower
than the starting compound
e.g. Hofmann rearrangement
CH3CH2

NH2

NaOH, Br2
CH3CH 2NH2
H2O

Neber rearrangement
R

H2
C C
N

R'
OTs

EtO

H
C

NH2O

R'

CH3CH2

H
C

R'

3.2 Determination of the presence of

intermediates
3.2.2 Detection of an intermediate
In many cases, intermediate cannot be isolated but can
be detected by IR, NMR, UV-Vis or other spectra.
Radical and triplet species can be detected by ESR and
by Chemically Induced Dynamic Nuclear Polarization
(CIDNP).
Radicals can also be detected by cis-trans isomerization
of stilbene.

Caution: Beware of non-intermediate species and

impurities which may give interference signals.
7

3.2 Determination of the presence of

intermediates
3.2.3 Trapping of an intermediate
In some cases, the suspected intermediate is known
to be one that reacts in a given way with a certain
compound.
Benzynes react with dienes in the Diels-Alder
reaction
O
Br

Li
(trap)

benzyne
8

3.2 Determination of the presence of

intermediates

Trapping an anion to determine

if the elimination of alkenes is
E2 or E1cb. ClHC CCl2
E1cb

OH
E2

ClC CCl2

ClC CCl

D2O
(trap)

D
ClC CCl2

3.2 Determination of the presence of

intermediates
Examples of free radical trapping agents are DPPH, oxygen
(O2), triphenylmethylradical (Ph3C), nitric oxide (NO), imine
oxide, iodine, hydroquinone and dinitrobenzene.
O2N
Ph2NN

NO2

O
PhHC N

O2N

DPPH

Imine Oxide

A radical reaction may proceed slower in the presence of air

if the free radical intermediate can be trapped by O 2.
10

3.2 Determination of the presence of

intermediates

Kinetic requirement of
k1 trapping
k2[x]
intermediate
B
A

k2'[x']

k'[x']?
D

- The intermediate B can be efficiently trapped by X

when k2 k2.
- The detection of D does not always guarantee the
formation of B intermediate as A may directly react
11
with X to form D.

3.2 Determination of the presence of

intermediates
3.2.4 Addition of a suspected intermediate
Perform a reaction by using a suspected intermediate
obtained by other means can be used for a negative
evidence.
e.g. von Ritcher reaction:
NO2

CO2H
von Ritcher
condition

CN

von Ritcher
condition

CO2H

12

3. Determination of Mechanism
3.3 Study of catalysis
Mechanism must be compatible with its catalysts ,
initiator and inhibitors.
Utilization of catalytic amount of peroxide, AIBN and
iodine usually suggests a radical mechanism.
Kinetic study of acid-base catalyzed reaction can reveal
the rate determination step (rds.) if it is involved with the
proton transfer process
3.3.1 General acid (or base) catalysis usually indicates that the
proton transfer process is the rds.
3.3.2 Specific acid (or base) catalysis usually indicates that
the proton transfer process is not the rds.
13

3.3.1 General acid (or base) catalysis

In general acid catalysis all species capable of donating
protons contribute to reaction rate acceleration.
The strongest acids (SH+) are most effective (k1 is the
highest).

Reactions in which proton transfer is rate-determining exhibit

general acid catalysis, for example diazonium coupling reactio
ns.
When keeping the pH at a constant level but changing the
buffer concentration a change in rate signals a general acid c
atalysis. (A constant rate is evidence for a specific acid cataly
st.)
14

3.3.2 Specific acid (or base) catalysis

In specific acid catalysis taking place in solvent S , the reaction rate is
proportional to the concentration of the protonated solvent molecules SH +.
The acid catalyst itself (AH) only contributes to the rate acceleration by
shifting the chemical equilibrium between solvent S and AH in favor of the
SH+ species. S + AH SH+ + A For example, in an aqueous buffer solution the reaction rate for reactants
R depends on the pH of the system but not on the concentrations of
different acids.

This type of chemical kinetics is observed when reactant R 1 in a fast

equilibrium with its conjugate acid R1H+ which proceeds to react slowly
with R2 to the reaction product for example in the acid catalyzed aldol
reaction.
15

3.3 Study of catalysis

Diazonium coupling shows general base
catalysis. Which step is the rds.?

Aldol reaction shows specific acid catalysis.

Which step is the rds.?

16

3. Determination of Mechanism
3.4 Labeling study
3.4.1 Group labeling: Easy to obtain starting materials
but the group change may alter the mechanism.
3.4.2 Isotope labeling: Difficult to obtain the starting
materials but no group alteration to affect the
mechanism. (Isotopic scrambling can complicate the
interpretation of the results.)
3.4.3 Crossover experiments: The experiments are
closely related to either group or isotope labeling.

17

3.4.1 Group labeling

Is Claisen rearrangement a [1,3]

or [3,3] sigmatropic
process?
O
OH
O

Ph

OH
Ph

OH

Ph

Ph
18

3.4.2 Isotope labeling

D can be detected by NMR, IR and MS
13C can be detected by 13C-NMR and MS
14C can be traced by its radio activity
15N can be detected by 15N-NMR
18O can be detected by MS
*
*
e.g. RCOO
- + BrCN
RCN
O-

O
R

O-

R
Br

R
Br

N C O
isolated
intermediate

C + C
N

19

3.4.2 Isotope labeling

Does the hydrolysis of ester
proceed through alkyl or
acyl
cleavage?
R
O
R
OH
R'

18

H218O

+ R'OH

O
R

18

O
O

R'

H2O

OH

+ R'18OH

Labeled water is
easier to find than
the labeled ester.

In these cases, the products can be easily

identified by MS.
20

Exercises

Do the following ethanolyses of -lactone involve alkyl or

acyl cleavage?
EtOH
O

H or OH
EtOH

neutral

HO

OEt
O

EtO

OH
O

Do the following hydrolyses of -lactone involve alkyl or

acyl cleavage?
H218O

H or OH
H218O

neutral

HO

OH

18

H18O

OH
O

21

3.4.3 Crossover Experiments

Use for distinguishing between intra- and intermolecular reaction

Crossover products
+
+
indicate intermolecular
reaction.
A'
B'
B'
A'
The method requires
No crossover product
identification of products
in the mixture.
The method cannot
+
B
A
B
A'
A
B
distinguish between an
+
+
+
intramolecular and
solvent cage reactions.
A'
B'
B'
A' + B'
A
A

crossover
products

22

3.4.3 Crossover Experiments

Is benzidine rearrangement an inter- or intramolecular process?
H H
N N
H2N

OR

H H
N N

OR

NH2

RO
H 2N

OR'

H H
N N

OR'

R'O
H 2N

OR
NH 2
OR'
NH 2

No crossover product indicates an intramolecular rearrangement

23

3.4.3 Crossover Experiments

Is 1,2 rearrangement of alkyl lithium an inter- or intramolecular
process?
PhH2C
Ph
Ph

Li
CH2Li

Ph
Ph

CH2Ph
CH2

Upon an addition of14C-labeled

- +
benzyl lithium (Ph*CH2 Li ), the
14
C-labeled product was
detected, indicating an
intermolecular process.

Ph
Ph
Ph

Li
CH2Li

Ph
Ph

Ph
CH2

Upon an addition of14Clabeled phenyl lithium (Ph*

+
Li ), no 14C-labeled product
was detected, indicating no
intermolecular process
involved.

This is called labeled fragment

addition technique

24

3. Determination of Mechanism
3.5 Isomeric selectivity study
Selectivity = Non-statistical distribution of
products
Specificity = Correspondence between isomeric
ratios of starting materials and products
Level of isomeric selectivity: chemoselectivity
regioselectivity diastereoselectivity
enantioselectivity
3.5.1 Regiochemical study
3.5.2 Stereochemical study
25

3.5.1 Regiochemical evidences

HX addition on alkenes
Br
+ HBr

Regioselectivity suggests
cationic mechanism.
Polar solvents increase the
reaction rate supporting
the polar mechanism.

+ HBr

Br

H2O2

Regioselectivity suggests
radical mechanism.
Solvent polarity has no
effect on the reaction rate
supporting the radical
mechanism.
26

3.5.1 Regiochemical evidences

Aromatic substitution by strong basic nucleophiles
Cl

NH2

NaNH2

Possible mechanisms: SNAr or benzyne

Cl NH 2
Cl

NH 2-

-Cl-

NH 2

(NH 2-)
-HCl

NH 2-

27

3.5.1 Regiochemical evidences

The benzyne mechanism was supported by regiochemical
evidences obtained from group and isotope lebeling
OMe

SNAr

OMe

NH 2

+ NH2 Cl

OMe

benzyne

14

NH 2

C label

NH2

NH2

Cl
NH2-

1:1 ratio

28

3.5.1 Stereochemical evidences

SN2 reaction
OTs

OAc

KOAc

and
OTs

OAc

The reaction is stereospecific

with 100% inversion indicating
that the reaction is concerted
and the nucleophile attacks
from the back side of the
leaving group.
The proposed transition state
is a trigonal bipyramid.

KOAc

Ph

AcO

OTs
H

CH3
29

3.5.1 Stereochemical evidences

Neighboring group participation (NGP)
HO

HCl

Cl

Cl

The reaction is not stereospecific but diastereoselective. Both

diastereomers give the same major product. The results
suggest a common intermediate for all diastereomers.
The stereochemistry is
controlled by the intermediate
not by the starting material.
Ph

Which one is the major product?

30

3.5.1 Stereochemical evidences

Neighboring group participation (NGP)

Ph

KOAc

Ph

only product
OAc

OTs
Ph

KOAc

Ph
+ enantiomer
OAc

OTs

Each reaction involves

NGP in which an
intermediate with 2
reactive sites is formed.

C2

homotopic

enantiotopic

31

3.5.1 Stereochemical evidences

Addition
Br2

Br

Br

Anti addition in which a bromonium ion was proposed as an

intermediate.
Br
32

3.5.1 Stereochemical evidences

Photorearrangement of spirofuran
COOMe
COOMe

OH

Possible mechanisms: pericyclic or biradical

COOMe
[1,3]
sigmatropic

COOMe
homo [1,5]
sigmatropic

OH

OH

Stereospecific product
COOMe
O

Racemic product

biradical

COOMe
O

COOMe
radical

recombination

33

OH

3. Determination of Mechanism
3.6 Kinetic studies
3.6.1 Measurements of rate
3.6.2 Mechanistic information obtained from
kinetic studies
3.6.3Rate law

34

3.6.2 Measurement of rate

Real Time Analysis by Periodic or Continuous Spectral
Readings
Quenching and Analyzing
Removal of Aliquots at Intervals

A+B
P
1 d [ A] 1 d [ B ]
1 d [ P]

Rate

N p dt
N B dt
N A dt

Rate k[ A] [ B ]
nA

nB

N = stoichiometric number
nA = order of reaction for reactant
A
ni = order of overall reaction

(Rate Expression)
k = rate constant
kobs = rate constant directly obtained
experimentally
molecularity = number of molecules
35
come together in a single step

3.6.2 Measurement of rate

Zeroth order

A
d [ A]

k0
dt

First order k
1
A

k0

A A0 k 0 t

[B]

A0
[A]

d [ A]

k1[ A]
dt

A A0 e k1t ln A ln A0 k1t
ln A0
ln A

slope = -k1

slope = -k0
t

36

3.6.2 Measurement of rate

Second order
2A

k2

d [ A]

2k 2 [ A]2
dt

1
1

2k 2 t
[ A] [ A]0

A+B

k2

d [ A]

k 2 [ A][ B ]
dt
Use pseudo first order: B0>>A0
[B] constant = B0
Treat like first order

d [ A]

(k 2 B0 )[ A]
dt

37

3.6.3 Mechanistic information obtained

from kinetic studies
Order of reaction can give information about which
molecules take part in rate determining step and the
previous steps.
Changes in rate constants upon structural and condition
changes can give much information about mechanisms.
(Linear free energy relationships)
From transition state theory, rate constants measured at
various temperature can lead to important energetic
parameters.

kr = A e-Ea/RT ; A = kT eS
h

/R ;

Ea = H

+ RT
38

3.6.3 Rate law

First order: Rate = k[A] (rds. is unimolecular process)
Second order: Rate = k[A]2 or Rate = k[A][B]
Order is for the whole reaction while molecularity is the
order for each step.
Rate law depends on the rate-determining step.
The first step is the rate-determining step:

A + B
I + B

slow
f ast

I
C

Rate = k[A][B]
39

3.6.1 Rate Law

The first step is a rapid equilibrium:

A + B
I + B

k1
k -1
k2

I
C

Rate = -d[A]/dt = k1[A][B] - k-1[I]

d[I]/dt = k1[A][B] - k-1[I] - k2[I][B] = k1[A][B] - (k-1 + k2[B])[I]
Steady state assumption: d[I]/dt = 0
[I] = k1[A][B]/(k-1 + k2[B])
Therefore
Rate = k1[A][B] - k1k-1[A][B]/(k-1 + k2[B])
Rate = k1k2[A][B]2/(k-1 + k2[B])
For rapid equilibrium in the first step k-1[I] k2[I][B] or k-1 k2[B]
Thus

Rate = K1k2[A][B]2

40

Exercise
Using the steady state assumption, derive a rate
expression for the following reaction if (a) the first step
is a rate determining step, (b) the first step is a fast
equilibrium.

k1

k-1

k2

Rate = -d[A]/dt = k1[A] - k-1[B]

d[B]/dt = k1[A] - k-1[B] - k2[B]
Steady state assumption d[B]/dt = 0
[B] = k1[A]/(k-1 + k2)
Rate = k1[A] - k-1k1[A]/(k-1 + k2)
Rate = k1k2[A ]/(k-1 + k2)
a)k-1 << k2: Rate ~ k1[A]
b)k2 << k-1: Rate ~ Kk2[A]

41

Exercise

Condensations
a) CH2(COOEt)2 + CH2O

OH-

HOCH2CH(COOEt)2

Rate = k[CH2(COOEt)2] [CH2O] [OH-]

The reaction between the enolate and formaldehyde is the rds.

b) 2CH3CHO

OH-

CH3CH(OH)CH2CHO

Rate = k[CH3CHO] [OH-]

The formation of the enolate is the rds.
Write a reasonable mechanism and specify the rds. of each
reaction.
42

3.7 Kinetic Isotope effects

3.7.1 Deuterium isotope effects (kH/kD) is the ratio between the
rate of reaction of the protonic substrate and that of the
corresponding deutero substrate.
A normal isotope effect has kH/kD > 1 indicating that
the reaction of the protonic substrate is faster than the
reaction of the corresponding deutero substrate.
An inverse isotope effect has kH/kD < 1 indicating that
the reaction of the protonic substrate is slower than
the reaction of the corresponding deutero substrate.
3.7.2 Primary isotope effect is observed in the reaction that its
rate determining step involves the breaking of the bond
connecting to the isotopic H.
The primary isotope effects usually have 2 kH/kD 7.
43

3.7.2 Primary isotope

effects

Origin of the primary isotope effects

H X kH/kD < 7 (late T.S)

R
R
R

H
H

X maximum kH/kD ~ 7
X kH/kD < 7 (early T.S)
E0

R H
R D

1
4

AB

m A mB
mA
m A mB

E0D E0H
44

3.7.2 Primary isotope

effects

Alcohol oxidation
R
R

OH
H (D)

+ H2CrO4

O
R

Gives kH/kD = 6.9

The transition state proposed for the rds. is as follow

O CrO3H

base
45

Exercise

Write a reasonable mechanism and specify the rate

determining step for the following reaction which
shows kH/kD 7
O
O
H+
CH3CCH2Br
CH3CCH3 + Br2

46

3.7 Kinetic Isotope effects

3.7.3 Secondary isotope effect is observed in the reaction that its

rate determining step does not involve the breaking of any
bond connecting to the isotopic H.
-secondary isotope effect usually has kH/kD in the range
0.7-1.5. It is the result of the greater vibration amplitude of
C-H bond comparing to C-D bond.

A normal -secondary isotope effect (kH/kD > 1) generally

suggests a rehybridization of the carbon connecting to the
isotopic H from sp3 to sp2 in the rate determining step.

An inverse -secondary isotope effect (kH/kD < 1) generally

suggests a rehybridization of the carbon connecting to the
isotopic H from sp2 to sp3 in the rate determining step.
-secondary isotope effect has kH/kD > 1. It is mainly
attributed to hyperconjugation.
47

3.7.3 Secondary isotope effect

Solvolysis of cyclopentyl tosylate
OTs

H (D)

H (D)

sp3C-H

sp2C-H

normal
Addition on aldehyde
O

Ph

CN-

H (D)

sp2C-H

(kH/kD = 1.17)

Ph

H (D)
CN

sp3C-H

(kH/kD = 0.833)
inverse

48

Summary of primary and secondary

kinetic isotope effects
(CH3)3CD + X
(CH3)2CDX
(CH3)2C=CD2 + H+
(CD3)2CHX

(CH3)3C. + DBr
+

(CH3)2CD + X+

(CH3)2CCD2H
+

(CD3)2CH + X-

primary
-secondary (normal)
-secondary (inverse)
-secondary

49

3.7 Kinetic Isotope effects

3.7.4Solvent isotope effects
Generally observed when a protic solvent e.g. D2O
or ROD is used.
kH/kD < 1 when the reaction involves a rapid
equilibrium protonation because the acidity of
D3O+ is greater than H3O+ (specific acid catalysis
can be used for confirmation)
kH/kD > 1 when proton transfer is the rate
determining step (general acid catalysis can be
used for confirmation)
Secondary solvent isotope effect can interfere the
interpretation. Solvent isotope effect is thus used
50
only as a supporting evidence.

Exercise
Write a reasonable mechanism for hydration of styrene and
predict which step is the rate determining step. Suggest 3
experiments and the expected results that can support the
proposed mechanism and rate determining step.

51