Chapter7b:(Radical(Reactions(andEnzyme(Catalysis ...

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Winter 2015 Chem 350: Statistical Mechanics and Chemical Kinetics Chapter 7b: Radical Reactions and Enzyme Catalysis and Inhibition 95 Chapter 7b: Radical Reactions and Enzyme Catalysis and Inhibition ...................................................... 95 Radical reactions, Radical Polymerization Explosions ............................................................................... 95 A Famous example: The HBr Reaction ................................................................................................... 98 Radical Chain Polymerization .............................................................................................................. 100 Radical Chain Explosions ...................................................................................................................... 102 Lindemann Mechanism for Unimolecular reactions............................................................................ 103 Catalysis, Enzyme Catalysis and Inhibition .............................................................................................. 105 Enzyme Inhibition ................................................................................................................................ 106 Heterogeneous Catalysis ..................................................................................................................... 108 Langmuir Adsorption Isotherms .......................................................................................................... 109 Langmuir Isotherm with dissociation .................................................................................................. 110 Chapter 7b: Radical Reactions and Enzyme Catalysis and Inhibition Radical reactions, Radical Polymerization Explosions Radical chain reactions: Let me discuss radical chain reactions by looking at a (simple) example. 4 2 3 CH Cl CH Cl HCl + + The proposed reaction mechanism (a set of elementary reactions) is as follows: a) Initialization: Cl 2 f 1 2Cl i b) Propagation: Cl i + CH 4 f 2 HCl + CH 3 i CH 3 i + Cl 2 f 3 CH 3 Cl + Cl i c) Termination: Cl i + Cl i b 1 Cl 2 (reverse of a)) But also CH 3 i + CH 3 i C 2 H 6 (not discussed in R&E). Other reactions involving radicals are possible eg. Cl i + HCl Cl 2 + H i (unlikely, much higher energy) Cl i + CH 3 Cl HCl + CH 2 Cl i These would definitely complicate the reaction mechanism.

Transcript of Chapter7b:(Radical(Reactions(andEnzyme(Catalysis ...

Winter  2015   Chem  350:  Statistical  Mechanics  and  Chemical  Kinetics    

Chapter  7b:  Radical  Reactions  and  Enzyme  Catalysis  and  Inhibition      

95  

Chapter  7b:  Radical  Reactions  and  Enzyme  Catalysis  and  Inhibition  ......................................................  95  Radical  reactions,  Radical  Polymerization  Explosions  ...............................................................................  95  

A  Famous  example:  The  HBr  Reaction  ...................................................................................................  98  Radical  Chain  Polymerization  ..............................................................................................................  100  Radical  Chain  Explosions  ......................................................................................................................  102  Lindemann  Mechanism  for  Unimolecular  reactions  ............................................................................  103  

Catalysis,  Enzyme  Catalysis  and  Inhibition  ..............................................................................................  105  Enzyme  Inhibition  ................................................................................................................................  106  Heterogeneous  Catalysis  .....................................................................................................................  108  

       Langmuir  Adsorption  Isotherms  ..........................................................................................................  109  Langmuir  Isotherm  with  dissociation  ..................................................................................................  110  

 Chapter  7b:  Radical  Reactions  and  Enzyme  Catalysis  and  Inhibition  

 Radical  reactions,  Radical  Polymerization  Explosions  

    Radical  chain  reactions:       Let  me  discuss  radical  chain  reactions  by  looking  at  a  (simple)  example.            

4 2 3CH Cl CH Cl HCl+ → +      

The  proposed  reaction  mechanism  (a  set  of  elementary  reactions)  is  as  follows:    

a) Initialization:   Cl2→

f12Cl i  

b) Propagation:   Cl i +CH4

f2

HCl +CH3i  

                                          CH3

i +Cl2f3

CH3Cl +Cl i  

c) Termination:   Cl i +Cl i →

b1

Cl2        (reverse  of  a))  

But  also   CH3i +CH3

i → C2H6  (not  discussed  in  R&E).    

Other  reactions  involving  radicals  are  possible  eg.           Cl i + HCl → Cl2 + H i   (unlikely,  much  higher  energy)  

      Cl i +CH3Cl → HCl +CH2Cl i     These  would  definitely  complicate  the  reaction  mechanism.    

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You  can  see  how  clever  the  mechanism  is.   Cl i  produces   CH3i ,  and   CH3

i  produces   Cl i  radicals.  One  radical  formed  can  hence  make  a  large  number  of  product  molecules.  This  aspect  governs  all  reactions  involving  radicals.  The  reaction  terminates  if  2  radicals  collide  and  react.  (This  is  why  anti-­‐oxidants  that  can  remove  radicals  can  be  highly  effective  even  in  small  doses.)    Let  me  set  up  the  reaction  mechanism  in  the  usual  systematic  fashion  

  1. Cl2!

f12Cl i ; R1 = f1[Cl2]− b1[Cl]2

 

  Cl i +CH4!

f2

HCl +CH3i ; R2 = f2[Cl i ][CH4]− b2[HCl][CH3

i ]  

  CH3

i +Cl2!f3

CH3Cl +Cl i; R3 = f3[CH3][Cl2]− b3[CH3Cl][Cl i]  

To  discuss  rates  of  reaction  one  applies  the  steady  state  approximation  to  the  intermediates  

CH3i ,   Cl i  

 

1)

d Cl i⎡⎣ ⎤⎦dt

= 2R1 − R2 + R3 = 0  

2)

d CH3i⎡⎣ ⎤⎦

dt= R2 − R3 = 0→ R2 = R3  

Using  the  second  equation  in  the  first  we  see  

   

d Cl i⎡⎣ ⎤⎦dt

= R1 = 0

2 f1 Cl2⎡⎣ ⎤⎦ − 2b1 Cl i⎡⎣ ⎤⎦2= 0

   

      →  

Cl i⎡⎣ ⎤⎦ =f1

b1

Cl2⎡⎣ ⎤⎦⎛

⎝⎜⎞

⎠⎟

1/2

 

       

   

d HCl⎡⎣ ⎤⎦dt

= R2

d CH3Cl⎡⎣ ⎤⎦dt

= R3 = R2 =d HCl⎡⎣ ⎤⎦

dt

 

               This  makes  sense.  If  the  propagation  steps  of  the  mechanism  dominate  the  rates  for  the  increase  in  cocentrations  for  concentrations   HCl⎡⎣ ⎤⎦ , CH3Cl⎡⎣ ⎤⎦  are  identical.  This  is  really  due  to  

the  fact  that  we  don’t  allow   CH3i  to  react  with  other  radicals  in  termination  reactions.  This  

simplifies  matters,  but  is  probably  not  quite  correct.  We  could  easily  examine  the  effects  in  Matlab  simulations.  (You  will  see  this  statement  more  often  in  this  section!)  If  we  neglect  the  backwards  rate  in  reaction  2,  we  find    

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  = f2 CH4⎡⎣ ⎤⎦ Cl i⎡⎣ ⎤⎦ =

d HCl⎡⎣ ⎤⎦dt

 

 

 

d HCl⎡⎣ ⎤⎦dt

= f2 CH4⎡⎣ ⎤⎦ Cl i⎡⎣ ⎤⎦ = f2

f1

b1

CH4⎡⎣ ⎤⎦ Cl2⎡⎣ ⎤⎦1/2

= keff CH4⎡⎣ ⎤⎦ Cl2⎡⎣ ⎤⎦1/2

 We  can  examine  the  rate  law  in  matlab,  and  examine  the  concentration  dependence  and  the  value  of  the  effective  rate  constant.  We  can  also  investigate  what  happens  if  we  include  backward  rates.      Let  me  discuss  some  more  examples.  The  math  gets  complicated  quickly.           C2H6 C2H4 + H2     Mechanism:  

o Initiation  :     1.   C2H6→

f12CH3

i  

2.   CH3

i +C2H6→f2

CH4 +C2H5i  

 o Propagation:        

3. C2H5

i →f3

C2H4 + H i

 

            4.   H i +C2H6→

f4

C2H5i + H2  

o Termination:           a)   Hi + H i → H2  

b=5)   Hi +C2H5

i f5⎯ →⎯ C2H6  

c)   Hi +C2H5

i → C2H4 + H2  

d)   C2H5i +C2H5

i → C2H4 +C2H6      

It  will  be  clear  that  to  include  all  reactions  is  complicated.  Easy  to  do  by  computer,  hard  by  hand.  If  one  only  considers  reaction  b)  for  termination,  one  obtains  reactions  considered  in  R&E  (9.15).  

 Apply  steady  state  to  the  radical  intermediates:  

 

d CH3 i⎡⎣ ⎤⎦dt

= 0 = 2 f1 C2H6⎡⎣ ⎤⎦ − f2 CH3i⎡⎣ ⎤⎦ C2H6⎡⎣ ⎤⎦  

    →

CH3i⎡⎣ ⎤⎦ = 2

f1

f2

  (constant!)  

If  we  would  also  include  reverse  of  reactions  1  and  2  this  would  no  longer  be  true!    

1)

d C2H5i⎡⎣ ⎤⎦

dt= 0 = R2 − R3 + R4 − R5  

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2)

d H i⎡⎣ ⎤⎦dt

= 0 = R3 − R4 − R5  

 Adding  1)  +  2)  

   

−2R5 + R2 = 0

−2 f5 H i⎡⎣ ⎤⎦ C2H5i⎡⎣ ⎤⎦ + f2 CH3

i⎡⎣ ⎤⎦ C2H6⎡⎣ ⎤⎦ = 0    

    use  

CH3i⎡⎣ ⎤⎦ = 2

f1

f2

 

     

H i⎡⎣ ⎤⎦ =

f1 C2H6⎡⎣ ⎤⎦f5 C2H5

i⎡⎣ ⎤⎦  

      Substitute  in  2)      

   

0 = f3 C2H5

i⎡⎣ ⎤⎦ −f4 f1

f5

C2H6⎡⎣ ⎤⎦2

C2H5i⎡⎣ ⎤⎦

− f1 C2H6⎡⎣ ⎤⎦  

  or   0 = f3 C2H5

i⎡⎣ ⎤⎦2− f1 C2H6⎡⎣ ⎤⎦

2C2H5

i⎡⎣ ⎤⎦ −f4 f1

f5

C2H6⎡⎣ ⎤⎦  

 

  This  is  a  quadratic  equation  for  

C2H5i⎡⎣ ⎤⎦ ,  which  can  be  solved,  using  the  positive  root,  and  

simplified  to  

     

C2H5i⎡⎣ ⎤⎦ = C2H6⎡⎣ ⎤⎦

f1

2 f3

+f1

2 f3

⎝⎜⎞

⎠⎟

2

+f1 f4

f3 f5

⎢⎢⎢

⎥⎥⎥  

          [ ]2 6effk C H=  

     

d C2H4⎡⎣ ⎤⎦dt

= f3 C2H5i⎡⎣ ⎤⎦ = f3keff C2H6⎡⎣ ⎤⎦  

     

d C2H6⎡⎣ ⎤⎦dt

= ... ( ) [ ]22 6effk C H=    

→  In  the  end  the  whole  reaction  is  first  order  reaction  for  [ ]2 6C H ,    just  as  if  we  would  react  ethane  as  

given  in  the  overall  reaction.    Kinetics  is  often  quite  a  puzzle  to  sort  out  experimentally.  Here  one  could  easily  go  astray.  Look  back  at  how  we  eventually  sorted  out  that  the  reaction  is  first  order  in  [ ]2 6C H  

!  

 Again  it  will  be  clear  how  quickly  things  become  complicated.        A  Famous  example:  The  HBr  Reaction    

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        H2 + Br2 2HBr     The  following  reaction  mechanism  describes  the  reaction  

1) Br2

b1

f12Br i  

2) Br i + H2

b2

f2

HBr + H i    (slowest)  

3) H i + Br2→

f3

HBr + Br i  (fast)  

4) H i + Br i →

f4

HBr  

5) H i + H i →

f5H2  

Reaction  3)  is  very  fast.  H  radicals  are  consumed  as  soon  as  they  are  produced.  This  means  their  concentration  is  very  small  [ ] 0H ≈ .  For  this  reason  we  can  neglect  reactions  4)  and  5)  

irrespective  of   4 5,f f  (

Br i⎡⎣ ⎤⎦  is  also  small).  

 

  →Apply  steady  state  to  

H i⎡⎣ ⎤⎦  

   

d H i⎡⎣ ⎤⎦dt

= r2 − r3 = 0  

    0 = f2 H2⎡⎣ ⎤⎦ Br i⎡⎣ ⎤⎦ − b2 HBr⎡⎣ ⎤⎦ H i⎡⎣ ⎤⎦ − f3 H i⎡⎣ ⎤⎦ Br2⎡⎣ ⎤⎦  

     

H i⎡⎣ ⎤⎦ =f2 H2⎡⎣ ⎤⎦ Br i⎡⎣ ⎤⎦

f3 Br2⎡⎣ ⎤⎦ + b2 HBr⎡⎣ ⎤⎦  

This  relation  can  be  checked  in  numerical  simulation  with   3f  large      

The  reactions  with   Br i  are  slower.  It  is  somewhat  dubious  if  one  can  make  further  approximations,  by  simply  assuming  the  steady  state  approximation.  

If  we  do  steady  state:  [ ]

1 2 30 2d Br

r r rdt

= = − +  

      Since  (see  above)   2 3r r=    →       1 0r =    

If  we  would  use  prequilibrium:     Br2 2Br i  (This  is  already  at  equilibrium  as          reactant!    We  would  assume  equilibrium  is  maintained  during  reaction.  This  seems  to  be  

a  reasonable  approximation.  )        →           1 0r =         Both  reasonings  lead  to  same  result  →   1 0r =  

f1 Br2⎡⎣ ⎤⎦ = b1 Br i⎡⎣ ⎤⎦

2  

 

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Br i⎡⎣ ⎤⎦ = f1 / b1 Br2⎡⎣ ⎤⎦

1/2  

      Also  this  relation  could  be  checked  in  numerical  simulation       For  the  rate  of  reaction  we  find  (use  the  formula  above  for  

H i⎡⎣ ⎤⎦ ):  

     

d HBr⎡⎣ ⎤⎦dt

= f2 H2⎡⎣ ⎤⎦ Br i⎡⎣ ⎤⎦ − b2 HBr⎡⎣ ⎤⎦ H i⎡⎣ ⎤⎦ + f3 H i⎡⎣ ⎤⎦ Br2⎡⎣ ⎤⎦  

       

= f2 H2⎡⎣ ⎤⎦ Br i⎡⎣ ⎤⎦ 1+f3 Br2⎡⎣ ⎤⎦ − b2 HBr⎡⎣ ⎤⎦( )f3 Br2⎡⎣ ⎤⎦ + b2 HBr⎡⎣ ⎤⎦( )

⎝⎜⎜

⎠⎟⎟  

        = f2 H2⎡⎣ ⎤⎦ Br i⎡⎣ ⎤⎦

2 f3 Br2⎡⎣ ⎤⎦f3 Br2⎡⎣ ⎤⎦ + b2 HBr⎡⎣ ⎤⎦

 

     

d HBr⎡⎣ ⎤⎦dt

=2 f2 H2⎡⎣ ⎤⎦ Br i⎡⎣ ⎤⎦

1+ b2 HBr⎡⎣ ⎤⎦ f3 Br2⎡⎣ ⎤⎦  

 

  Finally  we  substitute  

Br i⎡⎣ ⎤⎦ = f1 / b1 Br2⎡⎣ ⎤⎦1/2

 

     

d HBr⎡⎣ ⎤⎦dt

=2 f2 f1 / b1 H2⎡⎣ ⎤⎦ Br2⎡⎣ ⎤⎦

1/2

1+ b2 / f3( ) HBr⎡⎣ ⎤⎦ Br2⎡⎣ ⎤⎦( )      You  can  observe  the  integrated  rate  law  is  really  very  complicated  for  such  a  simple  reaction.  We  will  examine  the  reaction  in  Matlab!.  It  will  turn  out  that  it  is  crucial  to  have   Br2 , Br i  to  pre-­‐equilibrate  (as  they  would  in  practice).  It  is  an  interesting  experiment  to  equilibrate  reagents  at  temperature  T1  and  to  run  the  reaction  at  temperature  T2.  The  computer  can  simulate  this  case  as  effortlessly  as  ever,  but  the  above  tedious  derivation  may  no  longer  hold!  In  particular   Br2 , Br i

 would  initially  be  in  equilibrium  at  T1,  but  then  need  to  reach  a  new  equilibrium    at  T2.  At  this  stage  the  approximations  might  break  down.  We  can  verify  using  Matlab.      Radical  Chain  Polymerization    

Radical  chain  reactions  are  a  major  source  for  polymers,  for  example  polymerization  of  polyethylene  

      Initiation:     I2 → 2I i      or       CH3I → CH3

i + I i  

        Ii +C2H4 → ICH2CH2

i

        or  

        CH3i +C2H6 → CH3CH2CH2

i → ....         Propagation:        

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      ICH2CH2 C2H4( )n

CH2CH2i +C2H4 → ICH2CH2 C2H4( )n+1

CH2CH2i  

 The  polymer  grows  by  one  unit  in  each  reaction.  The  head  of  the  polymer  stays  a  (similar)  radical       Termination:  

a) Pni + Pm

i → Pn+m  

b) PnC2H2i + PmC2H2

i → PnCH2CH3 + PmCH = CH2  

c) C2H4 + PnCH2CH2i → C2H5

i +PnCH = CH2  

→  start  new  chain  from   C2H5i  

     

Cross  chain  formation  is  also  possible.    A  radical  might  attack  in  the  middle  of  the  chain,  or  extract  a  hydrogen  atom  from  the  middle.  Since  radicals  are  very  reactive,  many  different  products  can  be  formed.  Of  course  the  full  kinetics  is  complicated.    The  simplest  schematic  to  analyse  a  rate  equation  is    

   

d M i⎡⎣ ⎤⎦dt

= 0 = 2ki I⎡⎣ ⎤⎦ − 2kt M i⎡⎣ ⎤⎦2= 0    

M i⎡⎣ ⎤⎦ =

kt

ki

⎝⎜⎞

⎠⎟

1/2

I⎡⎣ ⎤⎦1/2

 

    M i  radical  concentration  of  any  kind    

d M i⎡⎣ ⎤⎦dt

= −kp M⎡⎣ ⎤⎦ M i⎡⎣ ⎤⎦  

  = −kp

kt

k1

⎝⎜⎞

⎠⎟

1/2

I⎡⎣ ⎤⎦1/2

M⎡⎣ ⎤⎦  

  [ ]effk M=     [ ]1/2~effk I  

      The  [ ]I concentration  then  determines  the  average  chain  length  n.  The  average  chain  

length  can  be  defined  as  the  ratio  of  the  rate  of  monomer  consumption  divided  by  the  rate  of  producing  new  radical  (or  reactive)  centers:  

       

n =

d M⎡⎣ ⎤⎦ dtd I i⎡⎣ ⎤⎦ dt

=−kp M⎡⎣ ⎤⎦ M i⎡⎣ ⎤⎦

2ki I⎡⎣ ⎤⎦  

             [ ] [ ]

[ ]

1/21/2

2

tp

i

i

kk I Mkk I

⎛ ⎞⎜ ⎟⎝ ⎠=        

[ ][ ]1/2

~k MI

 

     

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102  

    →  decreasing  [ ]I ,  initiator  of  radicals,  increases  the  chain  length.  Since  each   I  

    produces  2  radicals,  it  scales  with  [ ] 1/2I −  

   Radical  Chain  Explosions       A  famous  explosion  is   2 2 22H O H O+ →  

 The  reaction  is  exothermic  and  hence  the  heat  produced  raises  the  temperature  and  increases  the  rate  of  the  reaction.    This  is  a  plausible  reasoning,  but  heat  dissipates  quickly,  there  is  another  mechanistic  reason  for  the  occurrence  of  the  explosion:  branching  radials  or  radical  multiplication.    Reaction  mechanism:    

1) H2 +O2 → 2OH i  

1b)          Also   O2 → 2Oi    seems  relevant  (not  quoted  in  R&E,  O  atoms  are                                        present  always)  2) H2 +OH i → H i + H2O  

3) Hi +O2 → i O i +OH i  

4) iO i + H2 → OH i + H i   3)  and  4)  provide  additional  radicals!  

5) Ri +Wall → R −Wall  6) R1

i + R2i → R1R2     5)  and  6)  act  as  termination  

 The  key  to  a  possible  explosion  is  that  a  single  radical  might  produce  2  radicals,  including  O  atoms  which  are  like  a  bi-­‐radical.  Then  things  can  get  out  of  hand!    Let’s  make  a  very  rough  schematic  of  kinetics:    

      A+ B→

k1

Ri +C  

      Ri →

kb

nRi + P1     (branching)  

      Ri →

kt

P2     Here   n  is  an  integer,  the  “branching  efficiency”  

     

d Ri⎡⎣ ⎤⎦dt

= k1 A⎡⎣ ⎤⎦ B⎡⎣ ⎤⎦ + nkb Ri⎡⎣ ⎤⎦ − kb Ri⎡⎣ ⎤⎦ − kt Ri⎡⎣ ⎤⎦  

        = Γ + keff Ri⎡⎣ ⎤⎦    

    Now   effk  can  be  greater  or  less  than  zero:  

 

Winter  2015   Chem  350:  Statistical  Mechanics  and  Chemical  Kinetics    

Chapter  7b:  Radical  Reactions  and  Enzyme  Catalysis  and  Inhibition      

103  

  (Note  I  do  not  understand  this  model:  I  can  only  generate  two  radicals  from  an  initialization,  or    take  away  two  radicals  in  termination.   Presumably  this  complicates  matters  such  that  one    cannot  solve  the  model  anymore  (I  didn’t  try).  This  seems  a  real  issue  with  kinetics  models:  We  postulate  models  we  can  solve,  not  necessarily  models  that  are  realistic.  Anyway.)  

 If   0effk < radicals  gradually  disappear,  but  if   0effk > the  number  of  radicals  grows  over  time,  it  

is  like  a  population  growth  and  a  “radical  population  explosion”  can  occur.      Let’s  obtain  the  integrated  rate  law:  

       

d Ri⎡⎣ ⎤⎦dt

= Γ + keff Ri⎡⎣ ⎤⎦  

       

d Ri⎡⎣ ⎤⎦Γ + keff Ri⎡⎣ ⎤⎦

= dt  

       

d Ri⎡⎣ ⎤⎦Ri⎡⎣ ⎤⎦ + Γ keff

= keff dt  

        ln Ri⎡⎣ ⎤⎦ + Γ / keff( ) = keff t +C  

 

       

Ri⎡⎣ ⎤⎦ = Cekeff t − Γ / keff        At   0t = ,   Ri⎡⎣ ⎤⎦ = 0

            (note:    what  about  O  atoms?)    

        → Ri⎡⎣ ⎤⎦ =

Γkeff

ekeff t −1( )  

              The  model  only  provides  the  long  time  behavior:  growth  or  decay  (that  seems  reasonable  from  my  noted  criticism).  We  can  do  quite  realistic  simulations  in  Matlab,  and  simply  monitor  the  rate  of  radical  production.  Then  we  can  analyse  if  explosive  growth  does  occur.  It  becomes  a  mantra  in  these  lecures:  Numerical  simulations  are  relatively  straightforward.  Making  logical/consistent  analytical  models  is  much  harder.  They  probably  should  be  tested  against  numerical  simulations.  

   Lindemann  Mechanism  for  Unimolecular  reactions    

Winter  2015   Chem  350:  Statistical  Mechanics  and  Chemical  Kinetics    

Chapter  7b:  Radical  Reactions  and  Enzyme  Catalysis  and  Inhibition      

104  

Consider   A P→ .  Molecules   A  would  need  excess  energy  (from  collisions)  to  react.  One  possibility  is  that  the  reaction  is  really  bimolecular             A A P A+ → +  

             

d A⎡⎣ ⎤⎦dt

= b1 P⎡⎣ ⎤⎦ A⎡⎣ ⎤⎦ − f1 A⎡⎣ ⎤⎦2  

  This  would  yield  second  order  kinetics  which  is  typically  not  observed    Lindemann  suggested  an  alternative  mechanism  

        A+ A

b1

f1A*+A  

                     2

*f

A P→  

    *A :  vibrationally  excited  (for  example)  due  to  collisions    

  Then        [ ] [ ]2 *d P

f Adt

=  

   [ ] [ ] [ ][ ] [ ]2

1 1 2

** * 0

d Af A b A A f A

dt= − − =   (steady  state)  

      [ ] [ ][ ]2

1

2 1

*f A

Af b A

=+

 

       

     [ ] [ ]

[ ]2

2 1

2 1

d P f f Adt f b A

=+

 

If   [ ]1 2b A f>>  →  first  order  kinetics,  if  [ ]A  is  small  (low  pressure)  →  second  order  kinetics    

 An  immediate  generalization  of  the  Lindemann  mechanism  is  that   *A  is  formed  by  collisions  

with  other  species  M (e.g.  air  molecules).  

      A+ M

b1

f1A*+M  

                      A*→

f2

P  

  Then        

d P⎡⎣ ⎤⎦dt

=f1 f2 M⎡⎣ ⎤⎦ A⎡⎣ ⎤⎦f2 + b1 M⎡⎣ ⎤⎦

= keff A⎡⎣ ⎤⎦  

 

If   [ ]1 2b M f<<  (small  [ ]M )  ,   keff = f1 M⎡⎣ ⎤⎦ .    If   [ ]1 2b M f>>  ,   1 2

1eff

f fkb

=  

Winter  2015   Chem  350:  Statistical  Mechanics  and  Chemical  Kinetics    

Chapter  7b:  Radical  Reactions  and  Enzyme  Catalysis  and  Inhibition      

105  

       Catalysis,  Enzyme  Catalysis  and  Inhibition       Let  us  discuss  enzyme  catalysis.  The  kinetics  of  other  (homogenous)  catalysts  are  similar    

          S + E

b1

f1ES  

          ES→

f2

P + E  

Enzyme  E  binds  to  reactant/substrate  S,  yielding  the  complex  ES.  The  complex  ES  reacts  to  product  and  regenerates  enzyme/catalyst  E    

   

d P⎡⎣ ⎤⎦dt

= f2 ES⎡⎣ ⎤⎦    

[ ] [ ][ ] [ ] [ ]1 1 2 0d ES

f E S b ES f ESdt

= − − =          (steady  state)  

 

[ ] [ ][ ] [ ][ ]1

1 2 m

f E S E SES

b f K= =

+   1 2

1m

b fKf+=  (Michaelis  Constant)  

    Further  inside  is  gained  by  trying  to  express  in  terms  of  initial  concentrations           [ ] [ ] [ ] [ ]oS S P ES= + +   [ ] [ ] [ ]oE E ES= +  

      [ ] [ ] [ ] [ ]oS S P ES= − −   [ ] [ ] [ ]oE E ES= −  

    At  initial  stage  of  reaction  [ ]P  

is  small  (and  we  can  neglect)  

      Km = [E][S]

[ES]  

      [ ] [ ][ ] [ ] [ ]( ) [ ] [ ]( )m o oK ES E S S ES E ES= = − −  

        [ ][ ] [ ] [ ] [ ]( ) [ ]2o o o oS E ES S E ES= − + +  

 

Winter  2015   Chem  350:  Statistical  Mechanics  and  Chemical  Kinetics    

Chapter  7b:  Radical  Reactions  and  Enzyme  Catalysis  and  Inhibition      

106  

  If  we  also  assume  [ ]ES  is  small    

      →   [ ] [ ][ ][ ] [ ]o o

m o o

S EES

K E S=

+ +  

 

       [ ] [ ][ ]

[ ] [ ]2 o o

om o o

d P f S ER

dt K E S= =

+ +  

       [ ] [ ][ ][ ]2

1 m o o

o o o

K E SR f S E

+ +=  

    Typically  [ ] [ ]o oE S<<  

(very  little  amount  of  catalyst  or  enzyme)  

       [ ] [ ] [ ]2 2

1 1 1m

o o o o

KR f E S f E

= +  

     

    →  if  one  plots  1

oR  vs  

[ ]1

oS  

         

So  the  maximum  rate  is [ ]2 of E :  all  of  the  enzyme  is  bound  into  [ ]ES  and  reacts  to  products.  If  

[ ]oS  is  decreased,  the  rate  is  reduced  (not  all  of  the  enzyme  is  bound  to   S )    

In  enzyme  kinetics  1

oR  vs  

[ ]1

oS  is  referred  to  as  a  Lineweaver-­‐Burk  plot  and  is  used  to  extract  

the  Michaelis  constant   Km      Enzyme  Inhibition         Elementary  reactions:    

1) E + S ES             1 1,f b  2) ES P + E     2f      (fast)  

Winter  2015   Chem  350:  Statistical  Mechanics  and  Chemical  Kinetics    

Chapter  7b:  Radical  Reactions  and  Enzyme  Catalysis  and  Inhibition      

107  

3) EI E + I    [ ][ ][ ]I

E IK

EI=  

4) ESI ES + I    [ ][ ][ ]II

ES IK

ESI=  

5) ESI P + EI     3f    (assume  slow:  inhibition)    EI :  Inhibitor   I binds  to  the  active  site  → competitive  inhibition  ESI :  Inhibitor   I  binds  to  different  site,  but   ESI  does  not  react  to  P ,  or  slowly  ( 3 2f f<< )→  non  competitive  inhibition  

    Both  processes  can  happen  simultaneously  (mixed  inhibition).         Let’s  assume   3 0f ≈     Let  me  first  state  the  result,  and  then  derive.  The  reaction  rate   v  satisfies    

       [ ]

[ ]2

/o

II I m o

f Ev

K Sα α≈

+     1 2

1m

b fKb+=   [ ]max 2 ov f E=  

      Or      [ ]max max

1 1I mII

o

Kv v v S

αα= +  

 

 [ ]1II

IK

α = +  [ ]1IIII

IK

α = +   →      plot  1v    vs  

[ ]1

oS  →  extract  info  on   α I ,α II , KI , KII , Km  

    Derivation:  

     

EI⎡⎣ ⎤⎦ = E⎡⎣ ⎤⎦I⎡⎣ ⎤⎦

KI

    [ ] [ ] [ ]II

IESI E

K=  

      [ ] [ ] [ ] [ ] [ ]oE E EI ES ESI= + + +  

       [ ] [ ] [ ] [ ]1 1I II

I IE ES

K K⎛ ⎞ ⎛ ⎞

= + + +⎜ ⎟ ⎜ ⎟⎝ ⎠ ⎝ ⎠

 

        [ ] [ ] [ ]o I IIE E ESα α= +  

      Moreover:   [ ][ ] [ ] [ ]1 1 2 0f E S b ES f ES− − =  

        [ ] [ ][ ] [ ][ ]1

2 1

oo

m

E SfES E Sf b K

≈ =+

 

          [ ] [ ]( )[ ]o I II o mE S K Eα α= +  

        [ ] [ ][ ]( )o

I II o m

EE

S Kα α=

+  

Winter  2015   Chem  350:  Statistical  Mechanics  and  Chemical  Kinetics    

Chapter  7b:  Radical  Reactions  and  Enzyme  Catalysis  and  Inhibition      

108  

      [ ] [ ][ ]( ) [ ]2

2o m

oI II o m

f S Kv f ES E

S Kα α= = ⋅

+  

       [ ]

[ ] [ ]2 maxo

II I m o II I m o

f E vK S K Sα α α α

= =+ +

 

       

[ ]max max

1 1I mII

o

Kv v v S

αα= +  

    We  will  explore  enzyme  catalysis  using  Matlab.         Iα :    Competitive  →    change  of  slope  on  Lineweaver-­‐Burk  

IIα :  Non  competitive  →  change  of  intercept       We  will  see  this  works  in  a  beautiful  fashion,  using  a  Matlab  simulation  without  approximations.      Heterogeneous  Catalysis         (a  very  brief  glance  at  a  complicated  subject.  Not  discussed  in  class.  Will  not  be  on  final  exam)       Many  industrial  processes  are  run  using  a  solid  surface  as  a  catalyst,  often  a  metal.      

We  first  need  to  understand  something  about  the  adsorption  of  a  gas  on  a  surface.  In  reality,  adsorption  occurs  preferentially  near  an  edge  or  a  kink  on  the  surface,  as  there  are  more  atoms  to  bind  to  

         Let’s  first  estimate  how  often  gas  phase  molecules  collide  with  a  surface  atom.  From  kinetic  theory  of  gases  (not  treated  in  these  notes)  

   ( )

( )( )( )1/2 1/21

/2 / /

o ow

Z P PPZmkT T k M gmolπ −

= =⎡ ⎤⎣ ⎦

 

    24 2 12.63 10oZ m s− −= ⋅    Then  for   1 atmP = ,   300T K= ,   129M gmol−= → 27 2 13 10wZ m s− −= ⋅ .  This  is  the  number  of  collisions  per  unit  area  per  second    

21m  of  surface   19 2~ 10 atoms m− → 27 19 83 10 /10 ~ 3 10⋅ ⋅  collisions  per  atom  per  second    The  main  strategy  to  keep  a  surface  clean  would  be  to  reduce  the  pressure  (eg.  To   810 atm− )  

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Chapter  7b:  Radical  Reactions  and  Enzyme  Catalysis  and  Inhibition      

109  

A  large  array  of  experimental  techniques  exists  to  investigate  surfaces.  (Visit  Tong  Leung’s  lab  to  see  the  action!)    Two  types  of  adsorption  are  distinguished:  

a) Physisorption:  molecules  are  weakly  attached  to  the  surface  (~ 20 /kJ mol )  eg.  By  Van  der  Waals  or  electrostatic  forces.  

b) Chemisorption:  The  molecules  react  with  the  surfaces,  forming  chemical  bonds  (~ 200 /kJ mol ).  For  molecules  to  adsorb   HΔ  is  always  negative,  as   SΔ  (gas  →  surface)  is  always  less  than  0  it  follows   0G H T SΔ = Δ − Δ <  

 To  understand  kinetics  of  catalysis  on  surfaces,  we  first  need  to  understand  adsorption  itself.      Fractional  Coverage:  

     number of occupied adsorption sides

total number of adsorption sidesθ =  

                        Langmuir  Adsorption  Isotherms         Assumptions:  

o Adsorp  at  most  one  monolayer  o Surface  is  uniform  o No  interaction  between  adsorbates    

 All  of  these  assumptions  are  somewhat  dubious    

A g( ) + M surface( )

kd

ka

AM surface( )  

        dθdt

= ka PAN 1−θ( )− kd Nθ  

      ,a dk k :  rates  of  ad/desorption,     N :  total  number  of  adsorption  sites  

      AP :  partial  pressure  of   A    

    At  equilibrium   0ddtθ =  

        ( )1a A dk P N k Nθ θ− =  

        ( )a A d a ak P k k P θ= +  

 

       1

a A A

d a A A

k P KPk k P KP

θ = =+ +

  /a dK k k=      (equilibrium  constant)    

      Or  1AKP θ

θ=

−  

      Describes  fractional  coverage  as  a  function  of  partial  pressure    

Winter  2015   Chem  350:  Statistical  Mechanics  and  Chemical  Kinetics    

Chapter  7b:  Radical  Reactions  and  Enzyme  Catalysis  and  Inhibition      

110  

     

Other  expression  for  θ ,   ads

M

VV

θ =    (volume  of  adsorbed  gas/full  monolayer  coverage)  

         1

ads

M

V KPV KP

=+

 

          ( )1 ads MKP V KPV+ =  

          Vads = KPVM − KPVads  

    Divide  by   ads MKV V P  

         

1KVM

⋅ 1P= 1

Vads

− 1VM

 

    →plot  1P    vs  

1

adsV  

              K  can  also  be  measured  as  function  of  T .  This  gives  access  to   adsHΔ  

          2

ln adsHKT RT

Δ∂ =∂

  (thermo)  

   Langmuir  Isotherm  with  dissociation         If  a  molecule   2A  dissociates  when  adsorbing  on  the  surface,  we  have    

          A2 + M 2AM  

        dθdt

= ka PA2N 1−θ( )( )2

− kd Nθ( )2= 0    at  equilibrium  

          (2  empty  sides)  

        ka PA2

N 1−θ( )( )2= kd Nθ( )2

 

        ka PA2

= θ1−θ

⎛⎝⎜

⎞⎠⎟

2

 

       

ka PA2( )1/2

= θ1−θ

 

Winter  2015   Chem  350:  Statistical  Mechanics  and  Chemical  Kinetics    

Chapter  7b:  Radical  Reactions  and  Enzyme  Catalysis  and  Inhibition      

111  

     

       ( )( )

1/2

1/21a A

a A

k Pk P

θ =+

  1/2P dependence  rather  than   P