1. 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.
Occam’s razor: In the event that several hypotheses are found to fit the facts, the simplest one is given preference.

2. 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. 3. Determination of Mechanism
3.1 Identification of products
Mechanism must be compatible with its products including the by-product.
e.g. von Richter Rearrangement
At the first glance, the mechanism was though as a simple nucleophilic substitution of NO2 by CN- followed by the hydrolysis of CN- to CO2H
However,

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

5. The mechanism was then fixed as follow:

6. 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 Neber rearrangement

7. 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.

8. 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

9. 3.2 Determination of the presence of intermediates
Trapping an anion to determine if the elimination of alkenes is E2 or E1cb.

10. 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.
A radical reaction may proceed slower in the presence of air if the free radical intermediate can be trapped by O2.
Imine Oxide
DPPH

11. 3.2 Determination of the presence of intermediates
Kinetic requirement of intermediate trapping
- 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 with X to form D.

12. 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:

13. 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.

14. 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 reactions.
When keeping the pH at a constant level but changing the buffer concentration a change in rate signals a general acid catalysis. (A constant rate is evidence for a specific acid catalyst.)

15. 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 R1 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.

16. 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.?

17. 3. Determination of Mechanism
3.4 Labeling study Group labeling: Easy to obtain starting materials but the group change may alter the mechanism 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.) Crossover experiments: The experiments are closely related to either group or isotope labeling.

18. 3.4.1 Group labeling
Is Claisen rearrangement a [1,3] or [3,3] sigmatropic process?

19. 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.

20. 3.4.2 Isotope labeling
Does the hydrolysis of ester proceed through “alkyl” or “acyl” cleavage?
Labeled water is easier to find than the labeled ester.
In these cases, the products can be easily identified by MS.

21. Exercises
Do the following ethanolyses of -lactone involve “alkyl” or “acyl” cleavage?
Do the following hydrolyses of -lactone involve “alkyl” or “acyl” cleavage?

22. 3.4.3 Crossover Experiments
Use for distinguishing between intra- and intermolecular reaction
Crossover products indicate intermolecular reaction.
The method requires identification of products in the mixture.
The method cannot distinguish between an intramolecular and “solvent cage” reactions.
No crossover product

23. 3.4.3 Crossover Experiments
Is benzidine rearrangement an inter- or intramolecular process?
No crossover product indicates an intramolecular rearrangement

24. 3.4.3 Crossover Experiments
Is 1,2 rearrangement of alkyl lithium an inter- or intramolecular process?
Upon an addition of14C-labeled phenyl lithium (Ph*-Li+), no 14C-labeled product was detected, indicating no intermolecular process involved.
Upon an addition of14C-labeled benzyl lithium (Ph*CH2-Li+), the 14C-labeled product was detected, indicating an intermolecular process.
This is called labeled fragment addition technique

25. 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

26. 3.5.1 Regiochemical evidences
HX addition on alkenes
Regioselectivity suggests radical mechanism.
Solvent polarity has no effect on the reaction rate supporting the radical mechanism.
Regioselectivity suggests cationic mechanism.
Polar solvents increase the reaction rate supporting the polar mechanism.

27. 3.5.1 Regiochemical evidences
Aromatic substitution by strong basic nucleophiles
Possible mechanisms: SNAr or benzyne

28. 3.5.1 Regiochemical evidences
The benzyne mechanism was supported by regiochemical evidences obtained from group and isotope lebeling 
1:1 ratio

29. 3.5.1 Stereochemical evidences
SN2 reaction
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.
and

30. 3.5.1 Stereochemical evidences
Neighboring group participation (NGP)
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.
Which one is the major product?

31. 3.5.1 Stereochemical evidences
Neighboring group participation (NGP)
Each reaction involves NGP in which an intermediate with 2 reactive sites is formed.

32. 3.5.1 Stereochemical evidences
Addition
Anti addition in which a bromonium ion was proposed as an intermediate.

33. 3.5.1 Stereochemical evidences
Photorearrangement of spirofuran
Possible mechanisms: pericyclic or biradical
Stereospecific product 
Racemic product

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

35. 3.6.2 Measurement of rate (Rate Expression)
Real Time Analysis by Periodic or Continuous Spectral Readings
Quenching and Analyzing
Removal of Aliquots at Intervals
(Rate Expression)
N = stoichiometric number
nA = order of reaction for reactant A
ni = order of overall reaction
k = rate constant
kobs = rate constant directly obtained experimentally
molecularity = number of molecules come together in a single step

36. 3.6.2 Measurement of rate
Zeroth order
First order

37. Use pseudo first order: B0>>A0
3.6.2 Measurement of rate
Second order
Use pseudo first order: B0>>A0
[B] constant = B0
Treat like first order

38. 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. k r
= A e -E a
/RT ;
A = kT D
S /R E =
H RT h

39. 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:
Rate = k[A][B]

40. 3.6.1 Rate Law The first step is a rapid equilibrium:
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

41. Exercise Rate = -d[A]/dt = k1[A] - k-1[B]
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.
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)
k-1 << k2: Rate ~ k1[A]
k2 << k-1: Rate ~ Kk2[A]

42. Rate = k[CH2(COOEt)2] [CH2O] [OH-]
Exercise
Condensations a)
Rate = k[CH2(COOEt)2] [CH2O] [OH-]
The reaction between the enolate and formaldehyde is the rds. b)
Rate = k[CH3CHO] [OH-]
The formation of the enolate is the rds.
Write a reasonable mechanism and specify the rds. of each reaction.

43. 3.7 Kinetic Isotope effects
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.
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.

44. 3.7.2 Primary isotope effects
Origin of the primary isotope effects k H /k D
< 7 (early T.S)
< 7 (late T.S)
maximum k
~ 7 R X

45. 3.7.2 Primary isotope effects
Alcohol oxidation
Gives kH/kD = 6.9
The transition state proposed for the rds. is as follow

46. Exercise
Write a reasonable mechanism and specify the rate determining step for the following reaction which shows kH/kD  7

47. 3.7 Kinetic Isotope effects
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 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.

48. 3.7.3 Secondary isotope effect
Solvolysis of cyclopentyl tosylate
normal
Addition on aldehyde
sp3C-H sp2C-H (kH/kD = 1.17)
sp2C-H sp3C-H (kH/kD = 0.833)
inverse

49. Summary of primary and secondary kinetic isotope effects

50. 3.7 Kinetic Isotope effects
3.7.4 Solvent 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 only as a supporting evidence.

51. 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.