CHAPTER 36

Complex Reaction
Mechanisms

1
 CHAPTER OUTLINE
36.1 Reaction Mechanisms and Rate Laws
36.2 The Preequilibrium Approximation
36.3 The Lindemann Mechanism
36.4 Catalysis
36.5 Radical-Chain Reactions
36.6 Radical-Chain Polymerization

36.7 Explosions
36.8 Photochemistry
36.9 Electron Transfer 2
36.1 Reaction Mechanisms and Rate Laws
 Reaction mechanisms: the collection of individual kinetic
processes or steps involved in the transformation of reactants
into products.

 Simple reaction: a reaction mechanism that consists of a single

elementary step.

 Complex reaction: a reaction that occurs in two or more

elementary steps.

 Intermediates: the species that are not overall reaction products

but appear in the mechanism.

 Stoichiometric number: the number of times a given step occurs

in a reaction mechanism.
3
 2N2O5 4NO2  O2 Experimental rate law: R = k[N2O5]

One of the possible mechanisms:

k1
2 N2O5 NO2  NO3 (36.2)
k 1

k2
NO2  NO3 NO2  O2  NO (36.3)

) NO  NO3
k3
2NO2 (36.4)

2N2O5 4NO2  O2

 This mechanism is an example of a complex reaction.

 NO and NO3 are intermediates.

 Step 1 must occur twice for every occurrence of steps 2 and 3.

4
For a reaction mechanism to be considered valid, the mechanism
must be consistent with experimentally determined rate law.

 k1[ N 2O5 ]  k 1[ NO2 ][ NO3 ]  k N2O5 n (36.5)

1 d [ N 2 O5 ] 1
R
2 dt 2
Stoichiometric number of the reaction is not included in the differential rate expression!
Applying the steady-state approx. to the intermediates,
d [ NO]
 0  k2 [ NO2 ][ NO3 ]  k3[ NO][ NO3 ] (36.6)
dt

d [ NO3 ]
 0  k1[ N 2O5 ]  k1[ NO2 ][ NO3 ]  k2 [ NO2 ][ NO3 ] (36.7)
dt
 k3[ NO][ NO3 ]

From eq. (36.6) we obtain

k2 [ NO2 ]
[ NO]  (36.8)
k3
5
Substituting eq. (36.8) into eq. (36.7) yields
 k2 [ NO2 ] 
0  k1[ N 2O5 ]  k1[ NO2 ][ NO3 ]  k2 [ NO2 ][ NO3 ]  k3  [ NO3 ]
 k3 
k1[ N 2O5 ]
 [ NO ][ NO ]  (36.9)
k1  2k2
2 3

Substituting eq. (36.9) into eq. (36.5) results in

1  k1[ N 2O5 ]  
R   k1[ N 2O5 ]  k 1   
2  k 1  2k2  
k1k2
 [ N 2O5 ]  keff [ N 2O5 ]
k1  2k2

Consistent with the experimentally observed first-order dependence

on [N2O5]. The proposed mechanism might be right!

6
36.2 The Preequilibrium Approximation
kf kp
AB I P
kr
When kf, kr >> kp, the reaction can be envisioned as occurring in
two distinct steps:
1. The equilibrium between the reactants and the intermediate
is maintained during the course of the reaction.
2. The intermediate undergoes decay to form product.

kf [I]
Kc    [I]  Kc [A][ B]
kr [A][ B]

d [ P]
R  k p [ I ]  k p K c [A][ B]  keff [A][ B]
dt
7
 A Preequilibrium Example
2NO (g)  O2 (g) 2NO2 (g)
Experimental observations:
 R  k[NO]2[O2]  simple trimolecular reaction?
 As the T increases, R decreases  simple rxn. is not possible
The proposed mechanism that can explain experimental results:
kf
O=NN=O 2NO N2O2 + heat exothermic H < 0
kr
kp
O=O
N2O2  O2 2NO2 Valid!

kf [ N 2 O2 ]
Kc    [ N O
2 2 ]  K c [ NO]2

kr [ NO]2
1 d [ NO2 ]
R  k p [ N 2O2 ][ O2 ]  k p Kc [ NO]2 [O2 ]  keff [ NO]2 [O2 ] 8
2 dt
 36.3 The Lindemann Mechanism
A  fragments R  k[A] at high reactant conc.
How does the reactant acquire sufficient energy to decompose?
Bimolecular collision provides energy  Why first order?

d [ P]
 k 2 [ A* ]
Lindemann mechanism: dt
First step: Using steady-state approx.

A A k1 d [ A* ]
A*  A  k1[A]2  k1[A* ][ A]  k2 [A* ]  0
dt
Second step: k [ A ]2
 [A* ]  1

A*  A
k 1
A A (k1[A]  k2 )
k2
or A* P d [ P] k1k2 [A]2
 
dt k1[A] k 2 9
 d [ P] k1k2 [A]2

dt k1[A] k 2

At high reactant concentrations At low reactant concentrations

(k1[A] >> k2) (k1[A] << k2)

d [ P] k1k2 d [ P]
 [A]  k1[ A ]2
dt k 1 dt

 First order in [A], consistent with  Second order in [A]

experiment.

 Rate-limiting step is
 Rate-limiting step is
k A A k1
A*  A
A* 2 P
10
Alternative Approach for High Conc. Condition

At high concentration, one can assume

preequilibrium approximation:
Lindemann mechanism:

k1 A *A A *
First step:
K  
A A A A
k1
A*  A k 1 2

Second step:
 A *  A
k1
k 1
A*  A A A k1
k2
d P
or A* P
 k2 A *  A
k1k2
R
dt k1

11
Generalization of Lindemann Mechanism
k1
AM A*  M
k1
k2
A* P
If [M] remains approximately constant,

d [ P] k1k2 [A][ M ]
  kuni[A]
dt k1[ M ]  k 2

k1k2 [ M ] k1k2
where kuni   (36.34)
k1[ M ]  k2 k  k2
1
[M]
At high [M], k1[M] >> k2 At low [M], k1[M] << k2
k1k2
kuni  kuni  k1[ M]
k 1 12
 k1k2 Inverting (36.34) yields
kuni  1 k1  1  1
k 1    
kuni k1k2  k1  [ M]

kuni  k1[ M]

13
 36.4 Catalysis
 A catalyst increases reaction rate by providing an additional
reaction path way with lower activation energy.

 The catalyst is not consumed during the reaction.

d P 
k1  k 2 SC
SC SC dt
k1
d SC
SC
k2
PC  k1 SC  k 1 SC  k 2 SC  0
dt
k1 SC SC
 composite constant 
 
SC    K  k 1  k 2 
k 1  k 2 Km  m 
 k1 

d P  k 2 SC

dt Km
14
[S] and [C] are difficult to measure over the entire course of rxn.
Conservation of mass gives

S0  S  SC  P S  S0  SC  P

C0  C  SC
 C  C0  SC

K m SC  SC  S0  SC  PC0  SC

SC2  S0  C0  P Km SC C0 S0  P  0

Expt. Conditions: (1) [SC] is small (2) Concerning initial rate

SC  C0 S0

S0  C0  K m

d P k 2 S0 C0

 R0 
dt
 k 2 SC 
S0  C0  K m
15
 36.4.1 Case 1: [C]0 << [S]0
k 2 S0 C0 k 2 S0 C0
R0   R0 
S0  C0  K m S0  K m

S0  K m
R0  k 2 C0  Rmax

S0  K m
k C
R  2 0 S
0 0
Km
16
 k S C 1 S0  K m 1  Km  1
R0  2 0 0      
S0  K m R0 k 2 S0 C0 k2 C0  k2 C0  S0

1 1 K 1
  m
R0 Rmax Rmax S0

17
 36.4.2 Case 2: [C]0 >> [S]0

k 2 S0 C0 k 2 S0 C0

R0   R0 
S0  C0  K m C0  K m

 The rxn. rate is first order in [S]0.

 The rxn. rate can be zero or first order in [C]0.

 In catalysis studies, this limit is generally avoided.

18
36.4.3 Michaelis-Menten Enzyme Kinetics
Enzyme

substrate
19
 k1 k2
lock-and-key model ES ES EP
k1

Michaelis-Menten rate law (when [S]0 >> [E]0)

k 2 S0 E 0
R0  Km: Michaelis constant
S0  K m
When [S]0 >> Km,
R0  k2 E0  Rmax
k2 is called “turnover number”, which is the
max. numb. of substrate per unit time that
can be converted into product (1~105 s1).

Lineweaver-Burk equation
1 1 Km 1
 
R0 Rmax Rmax S0 20
36.1

21
1 1 K 1
  m
R0 Rmax Rmax S0

22
 Another way to evaluate Km if Rmax is known

k 2 S0 E 0 R S
R0   max 0
S0  K m S0  K m
If the initial rate is equal to one-half the maximum rate,
Rmax R S
 max 0
2 S0  K m
S0  K m  2S0

K m  S0

23
 36.4.4 Competitive Inhibition in Enzyme Catalysis
Competitive inhibitors structurally resemble the substrate and
can occupy the enzyme active site; however, they are nonreactive.
k1
ES ES
k1
k2
ES EP
k3
EI EI
k3

[E]0 = [E] + [EI] + [ES]

Applying preequilibrium approx. (assuming k1, k1, k3, k3 >> k2),
ES  k1
Ks 
ES  k1
 Km  E  K m ES
S
 k k 
 recall that Km  1 2 
 k1 

EI
EI   E I K m ES I 
Ki   
EI  SKi
24
Ki
 K m ES  K m ES I
E0  E EI ES    ES 
S SKi

 K m K m I 
 ES   1
 S SK i 

 ES  E0
K m K m [ I]
1 
S SK i

d [ P] k 2 E 0 k2 [S][ E]0
R0   k 2 [ES]  
dt 1
K m K m [ I]
  [ I] 
S SK i [S]  K m 1  Ki 
k2 [S]0 [E]0
  assuming [ES] and [P] are small 
 [ I]   
[S]0  K m 1    S0  S  ES  P  25
 K i 
 with inhibition without inhibition


k2 [S]0 [E]0 k 2 [S]0 [E]0
R0  R0 
 [ I]  [S]0  K m
[S]0  K m 1  
 Ki 

 [ I] 
K  K m 1  
*
m
 Ki 

Rmax S0 Rmax S0

R0  R0 
S0  K m* S0  K m

, K m*  S0 , K m  S0
Rmax Rmax
When R0  When R0 
2 2

1 1 K m* 1 1 1 Km 1
   
R0 Rmax Rmax S0 R0 Rmax Rmax S0

26
36.8

27
Competitive inhibition has been used in drug design for
antiviral, antibacterial, and antitumor applications.

Inhibitor

Active substrate used by bacteria to

synthesize folate.

28
 36.4.5 Homogeneous and Heterogeneous Catalysis
 A homogeneous catalyst is a catalyst that exists in the same
phase as the species involved in the reaction, and heterogeneous
catalysts exist in a different phase.

 An example of gas-phase homogeneous catalysis:

Catalytic depletion of ozone by atomic chlorine

k1
Cl  O3 ClO  O2
k2
ClO  O Cl  O2

O3  O 2O2

 A major source of Cl come from the photolysis of

chlorofluorocarbons (CFCl3, CF2Cl2) that are common refrigerants.
29
 For the uncatalyzed reaction,
Rnc  knc [O][O3 ] k nc  3.30  105 M 1s1 at 220 K 

For Cl catalyzed reaction,

d [Cl]
Cl  O3
k1
ClO  O2  0  k1[Cl][ O3 ]  k2 [ClO ][ O]
k2
dt
ClO  O Cl  O2
k [Cl][ O3 ]
O3  O 2O2 [ClO ]  1
k 2 [O ]

The sum of intermediate conc. [X]  [Cl]  [ClO ]

k2 [ X ][ O]
[Cl] 
k1[O3 ]  k2 [O]
In the stratosphere,
d [O 3 ] k k [X ][O][O3 ]
Rcat   k1[Cl][ O3 ]  1 2 [O3] >> [O]
dt k1[O3 ]  k2 [O] k1 = 1.56  1010
k2 = 2.44  1010
Rcat  k2 [X][O] 30
The ratio of catalyzed to uncatalyzed rxn. rats is

Rcat k [X]
 2
Rnc knc [O3 ]

In the stratosphere [O3] is roughly 103 greater than [X], thus

Rcat 2.44  1010 M 1s1 3

 1 1
 10  74
Rnc 3.30  10 M s
5

Through Cl catalysis, the rate of O3 loss is roughly two orders

of magnitude greater than the bimolecular reaction of O3 and
O directly.

31
 Heterogeneous catalysis
 Heterogeneous catalysts are extremely important in industrial
chemistry.
Fe catalyst
N2  3H2 2NH3
 In solid catalysis, adsorption of reactants to the solid surface
is an important process.

 A critical parameter in evaluating surface adsorption is the

fractional coverage, , defined as

# of adsorption sites occupied Vadsorbed( P )

 
total # of adsorption sites Vm ( P  )

 The variation in  with reactant-gas pressure P at fixed T is

called an adsorption isotherm. 32
 Langmuir model for adsorption (physisorption)
ka
R(g)  M(surface) RM(surface)
kd
Three approximations in Langmuir model:
1. Adsorption is complete once monolayer coverage has been reached.
2. All adsorption sites are equivalent and the surface is uniform.
3. Adsorption and desorption are uncooperative processes.

Rateadsorption  ka PN (1   )
K=
K=

Ratedesorption  kd N K=

At equilibriu m, Rateadsorption  Ratedesorption

ka P

ka P  kd
1 1 1
 1
KP 
 K P 36.11 33
KP  1 Langmuir isotherm
 Langmuir model for adsorption (chemisorption)
ka
R2(g)  2M(surface) 2RM(surface)
kd

Rateadsorption  ka PN 2 (1   )2

Ratedesorption  kd N 2 2

At equilibriu m, ka PN 2 (1   )2  kd N 2 2

ka P(1   )2  kd 2

KP(1   )2   2

KP (1   )  
36.12
KP

1  KP 34
 Enthalpy of adsorption Hads
A van’t Hoff plot of lnK vs. 1/T should provide reaction enthalpy
and entropy.
K  e  G RT
G
ln K  
RT
G  H  TS
H S
ln K   
RT R

To evaluate enthalpy of adsorption:

1) Collecting different Langmuir isotherm and evaluating K at
different T using 1/ = 1+1/KP
2) Using van’t Hoff plot to obtain Hads and Sads.
35
 Limitations of Langmuir model

 Surfaces are generally not uniform, resulting in the presence

of more than one type of adsorption site.

 The rate of adsorption and desorption may depend on the

occupation state of nearby adsorption sites.

 The adsorbates can diffuse on the surface.

36
36.2

37
 Vads KP
 
Vm KP  1

38
 Vads KP
 
Vm KP  1

39
40
 36.5 Radical-Chain Reactions
Thermal decomposition of ethane:
C2H6(g) C2H4(g)  H2(g)
Small amounts of methane (CH4) are also produced

Mechanism proposed by Rice and Herzfeld:

k1
Initiation step C2H6 2CH3
k2
Propagation steps CH3  C2H6 CH4  C2H5
k3
C2H5 C2H4  H
k4
H  C2H6 C2H5  H2
k5
Termination step H  C2H5 C2H6
41
 36.3

Initiation

Propagation

Termination

42
43
44
 36.6 Radical-Chain Polymerization
ki
Initiation I 2R
k1
R  M M1

kp
Propagation M1  M M2
Assuming kp is
kp
M2  M M3 independent of
polymer size.
kp
Mn1  M Mn

kt
Termination Mm  Mn Mmn

Assume that the monomer consumption is dominated by the propagation,

d [M]
Rate    k p [M][ M] 45
dt
The rate of activated monomer production is

 d [M]  Applying steady - state approx. to [R ]

   k1[R ][ M]
 dt  production d [R ]
 2ki [I]  k1[R ][ M]  0
dt
 d [M] 
   2 k i [ I] 2k
[R ][ M]  i [I]
 dt  production k1

The rate of activated monomer loss is equal to the rate of termination:

 d [M] 
   2kt [M]2 (36.110)
 dt  decay

The total differential rate expression for [M] is

d [M]
 2ki [I]  2kt [M]2  0 (steady-state approx.) (36.111)
dt
12
 ki 
 [M]    [I]1 2 (36.112)
 kt 
46
 d [M]
Rate    k p [M][ M] 12
dt  ki 
[M]    [I]1 2 eq. (36.112)
 ki 
12
 kt 
 k p   [I]1 2 [M]
 kt 

 Kinetic chain length () is a measure of the efficiency of polymerization.

rate of monomer consumptio n k p [M][ M] k p [M ]

v  
2ki kt  [ I]1 2
12
rate of active center production 2k i [ I]

s.s. aprox. eq.(36.112)

  when ki , kt , [I] 
Therefore, polymerization is usually carried out at minimal initiator
conc. such that the number of activated monomer is kept small.
47
 36.7 Explosions
 Two types of explosion:
a) thermal explosion
b) chain-branching explosion

 Important mechanistic components of 2H2(g)  O2(g)  2H2O(g)

Initiation: H2  O2 2OH

Propagation: H2  OH H  H2O

Branching: H  O2 OH  O

lead to explosion
O  H2 OH  H

Termination: H  O2  M HO2  M*

 The occurrence of explosions is dependent on T and P.

48
 thermal
explosion

chain-branching
explosion

radical-radical rxn.

49
A generic scheme for chain-branching rxn. is as follows:
ki
AB R
kb
R  R  P1  is branching efficiency

kt
R P2
d [ R ]
 ki [A][ B]  kb [ R]  kb [ R ]  kt [ R]
dt let   ki [A][ B]
keff  kb   1  kt
   keff [R ]

[ R ] t
1

0
  keff [R ]
d [R ]   dt
0
1 1
 (a  bx) dx  ln( a  bx )

 
b
 keff t
[R]  e 1
keff
50
 [R] 
keff

 keff t
e 1    ki [A][ B]
keff  kb   1  kt

Case 1: kt >> kb(  1) Case 2: kt << kb(  1)



lim [R ]  1  e  kt t
kt  kb ( 1) kt
 lim [R ] 
kb ( 1)  kt

kb   1

e kb  1t  1
[R] = kt at t   [R] increases exponentially leading
to explosion.
[R] will never become large enough
to support branching, and explosion
will not occur.
51
 36.8 Photochemistry
 Photochemical processes involve the initiation of a chemical
reaction through the absorption of a photon by an molecule.

 Photochemical reactions are important in a wide variety of areas,

such as visual process, photosynthesis, ozone production and
decomposition (atmosphere chemistry),…etc.

 The energy of a photon is given by Planck equation:

hc
E photon  hv 

 A mole of photons is referred to as an einstein.

 The intensity of light is generally defined as energy per unit area

per unit time.

Unit of light intensity: J s1 cm2 or W cm2 52

 36.8.1 Photophysical Processes
A + h  P
The rate of reactant photoexcitation is given by

d [ A] I abs1000
Rate    (in M s1) eq. 36.131
dt l
where Iabs is the intensity of absorbed light (in Einstein cm2 s1)
l is the path length of the sample (in cm)
constant 1000 converts cm3 to L

According to Beer-Lambert law,

I trans  I 010l [ A ]  I 0e 2.303l [ A ] where  is molar absorptivity of A

I abs  I 0  I trans  I 0 (1  e 2.303l [ A ] )

Series expansion
 (2.303l[ A]) 2  ex=1xx2/2!x3/3!…
 I 0 1  1  2.303l[ A]   
 2!  53
 36.8.1 Photophysical Processes
Assuming [A] is small and keeping only the first two terms, we get

I abs  I 0 (2.303)l[A]

Substitution into eq. 36.131

d [A]
Rate    I 0 ( 2303) [ A]
dt
[ A] t
1
  d [A]   I 0 (2303)  dt
[ A]0
[ A] 0

 [A]  [A]0 e  I 0 ( 2303)t  [A]0 e  kt

 Note that the absorption of light will result in the decay of reactant
concentration consistent with first-order kinetic behavior. 54
 36.8.1 Photophysical Processes
Sometimes it is more useful to discuss photochemical processes with
respect to the number of molecules as opposed to concentration, in
particularly when considering the photochemistry of individual molecules.

dA ( 2303)
Rate    I0 A
dt NA

 A  A 0 e  I 0 2303 N A t
 A 0 e  I 0 At

where A is known as the absorption cross section

the rate constant for excitation ka is equal to I0A
I0 in unit of photons cm2 s1

55
 36.8.1 Photophysical Processes
Jablonski diagram for photophysical processes

Paths for S1  S0
Path1: VR + fluorescence

Path2: ISC + VR + phosphorescence

Path3: IC + VR

Intersystem crossing
Internal conversion nonradiative
Vibrational relaxation (~100 fs) processes

(~109 s) radiative 56
(~106 s to seconds) processes
Fluorescence lifetime
1
f 
0

k f  kic  kisc
S

Quantum yield
kf
f 
0
 k  0

k f  kic  kisc
S f f

# of photon emitted

# of photon absorbed

57
 36.8.2 Fluorescence and Quenching
 Collisional quenching:
kq
S1  Q S0  Q Rq  kq[S1][Q]

 The lifetime and quantum yield become

1 kf
f  and f   k f f
k f  kic  kisc
S
 kq [Q] k f  kic  k  kq [Q]
S
isc

 Stern-Volmer equation:
kf
S1 S0  hv

The fluorescence intensity

 d [S1 ] 
   I f  k f [S1 ]
 dt  f 58
 S1 can be considered an intermediate and under continuous irradiation
[S1] will not change.

With quenching process

d [S1 ]
 0  ka [S0 ]  k f [S1 ]  kic [S1 ]  kisc
S
[S1 ]  kq [S1 ][ Q]
dt
ka [S0 ]
[S1 ] 
k f  kic  kisc
S
 kq [Q]

 d [S1 ]  k f ka [S0 ]
   I f  k f [S1 ]  If 
 dt  f k f  kic  kisc
S
 k q [Q ]

Without quenching process

k f ka [S0 ]
I 
0

k f  kic  kisc
f S

59
I 0f  k f ka [S0 ]  k f  kic  kisc
S
 k q [Q ]  k  k  k isc  kq [Q]
S
      f ic
 S 
I f  k f  kic  kisc  k f ka [S0 ]    S
 k f kic kisc

I 0f kq
 1 [Q]  1   f kq [Q]
0
Stern-Volmer eq.
If k f  kic  k S
isc

When kf >> kic and kSisc,

or = f0
0
I kq
f
 1 [Q]
If kf

A plot of If0/If against [Q] is called Stern-Volmer plot, providing

a measure of f0kq or kq/kf. 60
 36.8.3 Measurement of f
If we excite the system with a pulse of light, the decay of S1 can be
measured directly by monitoring the fluorescence intensity as a
function of time.
d [S1 ]
 k f [S1 ]  kic [S1 ]  kisc
S
[S1 ]  kq [Q][S1 ]
dt
d [S1 ] [S ]
 1
dt f
t  f
Fluorescence intensity [S1 ]  [S1 ]0 e
 d [S1 ] 
undergoes exponential    I f  k f [S1 ]
t  f  dt f
decay! I f  I f , 0e

When kf >> kic and kSisc,

1 1
f    k f  kq [Q]
k f  kq [Q] f
61
 pyrene

36.4

62
1
 k f  kq [Q]
f

63
 36.8.4 Single-Molecule Fluorescence
S0  S1
Confocal scanning microscope S1 S0 fluorescence Recovery of S0

Decay to nonfluorescent state, e.g. T1.

The fluorescence will completely disappear once the molecule

is photodestruction. 64
 36.8.5 Fluorescence Resonance Energy Transfer

 The transfer of excitation from one chromophore to another thereby

reducing the excited-state population of the initially photoexcited
chromophore and correspondingly the fluorescence from this
chromophore is referred as fluorescence resonance energy transfer
(FRET).

hv kf
D D* Without A f 
k f  knr
kf
D* D kf
With A  f w fret 
knr k f  knr  k fret
D* D
kfret Efficiency of excitation transfer is defined as
D* + A D + A*
 f w fret
kf’ Eff  1 
f
A* A
65
Eff  1 as kfret is large
36.8.5 Fluorescence Resonance Energy Transfer

What factors influence FRET efficiency?

Förster theory (1940s):

i) Distance between donor and acceptor
ii) Relative orientation between donor and acceptor
iii) Overlap between fluorescence band of donor and
absorption band of acceptor

r06
Eff  6 6
r0  r

where r is the distance between D and A

r0 is the distance at which transfer efficiency is 0.5
66
36.8.5 Fluorescence Resonance Energy Transfer
16
  J f
2

r0  8.79  10 
5
4

 (unit in angstrom) Eq. 36.163
 n 
where i)  depends on the relative orientation of transition dipole
moments (0 for perpendicular, 2 for parallel, and 1/3 for
random orientation)
ii) f is the fluorescence quantum yield
iii) n is refractive index of the medium
iv) J is the spectral overlap integral

J    A ( ) FD ( )4d

67
36.8.5 Fluorescence Resonance Energy Transfer

68
When using FRET to measure distance, it is critical to choose a
donor/acceptor pair whose r0 is close to the length scale of interest.

For r >> r0, For r0 >> r,

r06 r06
Eff  6 6  0 Eff  6 6  1
r0  r r0  r

f of donor will be unaffected f of donor will be too small

by the presence of acceptor. to be detected.
EXAMPLE PROBLEM 36.5
You are designing a FRET experiment to determine the magnitude of the
structural change introduced by substrate binding to an enzyme. Using
site-specific mutagenesis, you have constructed a mutant form of the
enzyme that possesses a single tyrosine residue and a single tryptophan
residue, and these residues are separated by 11 Å. You would like to
determine if the distance between these residues changes with substrate
binding. The fluorescence of tyrosine overlaps with the tryptophan
absorption; therefore, these two amino acids form a FRET pair for which r0
= 9 Å, determined using the absorption and emission spectra in
combination with Equation (36.163). Calculate the FRET efficiency at 11 Å
separation, and how much this distance must increase in order for the
efficiency to decrease by 20%, the experimental detection limit.
Solution
96
r06 96 Eff  0.18  6 6
Eff  6 6  6  0.23 9 r
r0  r 9  116
r  11.6 angstrom
This FRET pair is not a good choice!
70
 36.8.5 Fluorescence Resonance Energy Transfer
Light-harvesting complex II
Light-harvesting pigments

chlorophyll
protein

-carotene

phycoerythrin FRET
Transformation of photon
energy into chemical energy 71
(electron transfer)
 36.8.6 Photochemical Processes
 A photochemical reaction can be viewed kinetically as another reaction
branch resulting in decay of S1.

Rphotochem.  k photo
S
[S1 ]

 The extent of photochemistry is quantified by the overall quantum yield,

, which is defined as the number of reactant molecules consumed in
photochemical processes per photon absorbed.

 The overall quantum yield can be greater than one.

HI  h H  I

H  HI H2  I

I  I I2
2 72
36.6

73
74
 36.9 Electron Transfer
D+A D+ + A
Rate  ksep [ D A ]
Kinetic Model
d [ D  A ]
 ket [ DA]  kbet [ D  A ]  ksep [ D  A ]  0
ka dt
D+A DA
kd ket [ DA]
 
 [D A ] 
kbet  ksep
ket
DA D+A d [ DA]
kb-et  ka [ D ][ A]  kd [ DA]  ket [ DA]  kbet [ D  A ]  0
dt
ksep ka [ D ][ A]  kbet [ D  A ]
D + A D+ + A  [ DA] 
kd  ket
 k   k [ D ][ A]  k [ D A ]
 

 [D A ]   et   a b  et

 k  k  kd  ket
 bet sep   75
 ket ka
 [ D  A ]  [ D][ A]
kbet kd  ksepkd  ksepket

ksepket ka
 Rate  [ D][ A]
kbet kd  ksepkd  ksepket

ksepket ka ket ka
If ksep >> kb-et, then Rate  [ D ][ A]  [ D][ A]
kbet kd  ksepkd  ksepket kd  ket

Case I: ket >> kd Case II: ket << kd

ket ka ket ka ket ka

Rate  [ D ][ A]  ka [ D ][ A] Rate  [ D ][ A]  [ D ][ A]
kd  ket kd  ket kd

Electron transfer becomes a Rate  ket K D ADA[ D][ A]

diffusion controlled reaction!

76
 36.9.2 Marcus Theory (1992 Nobel Prize)

For the system in which the donor and acceptor are fixed in a given
distance, the rate constant of electron transfer is

DA D+A
 G* kT 
ket  e
G*
G* 
G 
 
2 G

4
where  is called reorganization energy, the change in Gibbs energy
accompanying geometric relaxation of solvent and solute during the ET
process.
 Notice that the Gibbs energy of activation will be at a minimum when
G = 
77
 D+A
DA
DA D +A


G
G* G G* G* 
ket  G

G
G*
G*
G =  ket 
G

Electron transfer is barrierless!

ket is maximal! Marcus inverted regime! 78
Experimental evidence for Marcus inverted regime

79
EXAMPLE PROBLEM 36.7
The experimental results presented above demonstrate that a maximum in
the rate constant for electron transfer (~2  109 s1) occurs when G =
1.2 eV. Given this observation, estimate the rate constant for electron
transfer when 2-naphthoquinoyl is employed as the acceptor for which
G = 1.93 eV (experimental temperature is 296 K and assuming  is a
constant).
Solution
The maximal rate occurs at G =  = 1.2 eV.

G* 
G 
 
2


( 1.93 eV  1.20 eV )2
 0.111 eV
4 4(1.20 eV )

 G1*.93eV kT 1.601019 J
k1.93 eV e 0.111eV  1.3810 23 JK 1 296K
 0
e 1eV
 0.0129
kmax e

k1.93 eV  kmax  0.0129  (2  109 s1 )( 0.0129)  2.58  107 s1 80